The beginnings of the Department of Morphology, Systematics and Phylogeny of Animals are linked to the formation of the Department of Zoology within the Zoological Institute at the Belgrade University. Then the Department of Zoology and Physiology (later the Department of Zoology) of the Biology Department of the Faculty of Natural Sciences was formed. In the 1970s, the department was renamed the Department of Comparative Morphology and Systematics of Animals, and new subjects and modern forms of teaching were introduced at the department. Since 2002, the Department has had its current name - the Department of Morphology, Systematics and Phylogeny of Animals. The names of famous zoologists, Dr. Živojin Đorđević, Dr. Siniša Stanković, Dr. Milutin Radovanović, Dr. Simeun Grozdanić and others are associated with the work of the Department.

Teaching at the basic academic studies is carried out within the framework of the mandatory subjects Anatomy and Morphology of Chordates, Systematics and Phylogeny of Chordates (study groups Biology and Ecology), Invertebrate Zoology and Vertebrate Zoology (study group Molecular Biology and Physiology), as well as in a number of elective subjects. Members of the Department are involved in mentoring work with students in the subject Professional Research Project, as well as within the Center for Support of Educational Development.

Since the introduction of master's studies, the Department initially had two educational modules: Morphology, systematics and phylogeny of zoological taxa (for the Biology study group) and Aquatic Zoology (for the Biology and Ecology study groups). Currently, master's studies are organized in cooperation with two departments of the Institute of Zoology, in the Zoology module.

The department organizes field teaching in basic academic studies within the course Field and Laboratory Practicum in Vertebrate Biology, as well as in master's studies, within the course Field and Laboratory Practicum.

Doctoral studies were initially organized within the study program Morphology, Systematics and Phylogeny of Animals, in two modules: Morphology of Animals and Systematics and Phylogeny of Animals. Today, doctoral studies are organized within the study program Biology with two modules: Zoology and Fisheries Biology with Basics of Aquaculture.

Members of the Department are authors and reviewers of several textbooks, practical courses and monographs. Until 2019, scientific activities at the Department were carried out within the narrow scientific field of Morphology, systematics and phylogeny of animals, and since then they have been carried out within the narrow scientific field of Zoology.

Scientific research covers the areas of phylogeny, evolutionary morphology, population biology and ethology, biology of individual groups of fish, etc. Research is also being conducted in fisheries and conservation biology. In recent years, the focus of scientific work has been on the application of molecular methods, computed tomography methods, geometric morphometry and other modern approaches in the reconstruction of phylogenetic relationships and morphological changes. Part of the activity is also carried out within the Center for Genotyping of Fishery Resources.

The Department collaborates with a large number of institutions: the Institute for Biological Research "Siniša Stanković", the Institute for Medical Research, the Institute for Marine Biology of the University of Montenegro, the Institute "Ruđer Bošković" of the University of Zagreb, the Dutch National Center for Biodiversity "Naturalis" in Leiden, the Institute of Biology and Ecology of the Bulgarian Academy of Sciences, the Hellenic Center for Marine Research, the "Jožef Štefan" Institute and the Faculty of Biotechnology of the University of Ljubljana, Comenius University in Bratislava, as well as with the universities of Skopje, Bihać, Kragujevac and Banja Luka. Members of the Department are the recipients of seven Rufford Foundation grants and three SYTHESYS projects and are engaged in a large number of domestic and international projects in the field of fundamental and applied science and popularization of science.