The Scientific Council acts in an advisory capacity expressing preliminary scientific and technical opinions regarding research programmes and upon conclusion of the activity carried out by the personnel of the Institute and the personnel associated with it. This assessment is carried out in strict compliance with the methodology and actions envisaged by the National Agency for the Evaluation of Universities and Research Institutes (ANVUR) and, as far as may be applicable, by the independent rating organisation in compliance with Art. 14 and Art. 74, paragraph 4 of Law 150/2009.

The Scientific Council is composed of seven members: scientists from Italy and abroad of international renown, with special expertise and experience in the fields of biology and/or ecology. The majority of the members of the Scientific Council are selected from among the persons referred to in the preceding paragraph from public or private foreign research organisations. The Chair convenes the meetings of the Scientific Council and, after consulting the President of the SZN, establishes the order of the day.

The Scientific Council is appointed by the Administration Board upon recommendation by the President, who selects the members of the Scientific Council after consultation with the Council of Departments and seeks the binding opinion of the Accademia dei Lincei on the proposal to be submitted to the Executive Board.

The members of the Scientific Council remain in office for three years and may be reappointed twice.

The Scientific Council:

a. expresses its opinion on the overall scientific or sectoral strategy of the Institute, in particular on the ten‐year Strategic Vision Document and the Three‐Year Plan of Activity;
b. expresses its opinion on the constitution of the Departments and related research programmes;
c. expresses opinions on the projected human resources needs;
d. expresses its opinion on the content of educational activities;
e. expresses its opinion on the participation of the Institute in companies, consortia, and foundations;
f. must express its opinion on the evaluation procedures of researchers and technologists at the Stazione Zoologica, taking into account the methodology developed by ANVUR and, as far as is applicable, by the independent rating organisation under Art. 14 and Art. 74, paragraph 4 of Law 150/2009;
g. regularly assesses the results of the research work of the Institute, including activities undertaken in relation to the objectives set out in the Three‐Year Plan of Activity;
h. performs all the consultative activities assigned to it by the regulations of the Institute and the Administration Board.

The opinions and findings of the Scientific Council are communicated to the Executive Board together with a report by the Chair.

The President of the Stazione Zoologica may be invited to attend meetings of the Scientific Council without the right to vote.

The Scientific Council may meet using IT systems, as described in Art. 7, paragraph 9 of the SZN Statute.

The new organizational scheme of the Stazione Zoologica, established in 1967, takes some time to be applied, in the meantime, in 1976, a new director was appointed, Alberto Monroy, with the difficult task of re-establishing the prestige of the Institute, through new international partnerships, based on a solid internal scientific program. The main task which the new director is facing is to give a new dynamism to the scientific 'old lady', given that the traditional model of operation clearly showed the signs of the time and was unable to meet the new demands of scientific research.

Even in the era of molecular biology, the variety of organ systems in marine animals continued to offer a greater diversity of form and function, diversity is necessary for the fundamental properties of living systems.

And this is the major scientific challenge of the late' 70s and early '80s. The ensemble of life processes that had characterized the scientific problems of the Stazione Zoologica (fertilization and development, evolution, memory, nerve transmission) had to be reinterpreted in molecular terms, with new conceptual tools (information, program, gene regulation) and technicians (electron microscopy, macromolecular chemistry and then molecular engineering). What the Stazione Zoologica needs is a new framework for international cooperation, an effort to bring the frontiers of research in the scientific life of the institute, with the increased participation of internal scientists in international programs.  In the two decades between 1960 and 1980 the Stazione Zoologica lays the groundwork for a fundamental structural change. The ‘table system’ which for a century had ensured the economic base and the internationality, changed and the focus is also on internal research programs. However, only the research focus changed, not the international character. If until 1968 the internationalism was based on guest researchers, during the following years this character is guaranteed through collaborations with foreign colleagues and institutions. The new scientific and technical structure, from the fishermen, to the library, the laboratory technicians and researchers of course shows a remarkable ability to adapt quickly to new research approaches. What in the first century of the history of the Stazione Zoologica had been a duty to satisfy the requirements of visiting researchers, becomes a way to build up new projects and international collaborations.

Ecology is a focal point in the new development and the Stazione Zoologica becomes an obligatory reference point for every program on the ecology of the Mediterranean, while the acquired skills can be used in other ecological contexts, including the Antarctic.

But it was difficult to change the objectives and mode of operation of an entire institute, bringing it new blood and new energy. The growing financial constraints and institutional difficulties become a major obstacle to the scientific life of the Stazione Zoologica. A new financial and institutional leap is needed.

The Italian Parliament approved in 1982 a special law in favor of the Stazione Zoologica, which provides an increase in funding and recognizes the status of 'Special Scientific Institution' of public interest, under the supervision and control of the Ministry of Universities and Scientific and Technological Research. However, the Institute maintains a large scientific autonomy.
In the same year (1982), the Institute was renamed "Stazione Zoologica Anton Dohrn", which should not only be considered a tribute to the great accomplishment of Anton Dohrn, but also the acknowledgement of his aim of furthering research in a lab Research freed from national, philosophical or disciplinary frontiers.

The management of the Zoological Station is entrusted to a President, a Director and an Adminstrative Council. An International Scientific Council was created. In 1987 Gaetano Salvatore was appointed as President.

The internal structure organization is remodeled, as to combine the two aims which have long had been considered as contradictory: on one hand, the emphasis was placed on the Stazione’s in-house scientific activity, and the other, on national and international cooperation. Special attention is put in the development of new laboratories at the frontier of biology, such as Molecular Biology and Biotechnologies, in the promotion and participation in national and international projects aimed at solving problems related to the safeguarding the marine environment and the rational exploitation of marine resources.

The training programs, that, for a long time, had remained a secondary aspect of the activities of the Stazione Zoologica, become a priority. Regular, specialized courses conferences and seminars are promoted and organized, together with a specialized postdoctoral training of Italian and foreign scientific and technical staff.

Anton Dohrn had created the station with the departments of Zoology, Botany and Physiology. The new structure of the research laboratories included Biochemistry and Molecular Biology, Neurobiology, Biological Oceanography, Marine Botany, Cell Biology, Ecophysiology and Benthic Ecology. The technical facilities include one of the best libraries in the field of marine biology and related fields, the Historical Archives and Scientific Collections (a museum with about 3500 specimens of the Gulf of Naples, some of which are very rare, an herbarium, which served as an archive for historically important material, as well as the permanent location of holotypes of new species discovered in the Gulf of Naples).

Research at the Stazione Zoologica had always focused on two aspects of marine organisms: on one hand their structures, functions and habits are studied to further knowledge on living organisms in the Mediterranean, on the other, these organisms have the tools to push forward the knowledge on fundamental processes of life.

Fundamental biological research is associated with the study of the opportunities to use biotechnology for the use of marine natural resources, such as the artificial culture of invertebrates, the use of biologically active substances, the study of the marine environment in relation to biodiversity, centered on complex ecosystems such as the seagrass Posidonia oceanica.

After World War II, science and especially the biomedical sciences are expanding at an impressive pace and on an ever expanding institutional and economic scale. The number of scientists increases rapidly, and the costs of equipments and laboratory materials increased rapidly. The era of romantic science is over and the ideals of scientific research changed from the individual linked to individual dreams and projects to a full-scale collective effort.

The Stazione Zoologica remains a reference at the international level, and 'the Neapolitan experience' continues to be considered a necessary step for brilliant scientists. This is especially true for Italian biology and for the University of Naples; the Stazione Zoologica for many of Italian researchers is the way to get in contact with advanced biological research, thanks to the presence in Naples of visiting researchers and an extraordinary library. The international character of the institution is maintained thanks to several scientific collaborations, first of all with the Marine Biological Laboratory in Woods Hole Marine Biology and the British marine biology laboratories.

However, the ‘tables system’ produced inevitable fragmentation of research programs and an expensive dispersal of experimental apparatus, since each researcher comes with its own project and tries in Naples to get the best conditions to realize it. This produces a large diversity of research programs, which depend on the scientists who occupy the various tables provided by their governments, with no continuity that could amortize the major investments made necessary by the new type of biological research. Some heterogeneity existed previously, but it increases again after World War II, following the multiplication of the lines of biology research, which is becoming the world's leading science. This produces a hard financial crisis.

It becomes clear that the Stazione Zoologica needs a new administrative and institutional structure, to ensure a solid  financial and permanent basis. For almost a century the Italian government had continued to recognize the unique character of the Stazione Zoologica, a private institution in an international context. But in the new science context, this situation is not sustainable anymore. In 1967 the Italian government entrusted the management of the Institute to a ‘Commissario Straordinario’.