Since the opening of the Institute in 1947, ecology has been nurtured and developed as a separate research area. The Department of Ecology incorporates the most significant findings gained from complex stationary ecosystem research. The experience acquired is the result of the work of phytoecologists and zooecologists, who were organised into four departments within the Institute (the Department of Physiological and Biochemical Plant Ecology, the Department of Phytoecology, the Department of Zooecology, and the Department of Entomology) for many years. The work and dedication of the founders, primarily the academic Siniša Stanković, but also Prof. Milorad Janković, Dr Vojislav Mišić and Prof. Maksim Todorović, led to development in various fields.

Today, the Department of Ecology comprises researchers that are divided into two groups: phytoecology and zooecology.

Phytoecological research integrates ecophysiological plant research and research into biodiversity. Ecophysiological research focuses on: defining limiting environmental factors; analysing the morphological, anatomical, physiological, biochemical, and molecular response of plant species to anthropogenically-induced habitat degradation; identifying plant species which reflect changes in the quality of the environment through their ecophysiological adaptations and allelopathic interactions; and defining their ecophysiological potential to survive in anthropogenically altered conditions. Research concentrates on defining ecologically based principles for neutralising or reducing disturbances in the functioning of ecosystems and restoring biodiversity in anthropogenically disturbed areas. It includes different types of disturbed habitats: disturbed forest ecosystems, urban and riparian zones exposed to pollutants, ash and slag deposits at thermal power plants, and different types of natural habitats. As model organisms for our research, autochthonous and allochthonous plant species (indicators) which give a characteristic representation of a certain habitat, or a certain anthropogenic activity, are used. Research methods integrate field (in vivo and in situ) and laboratory methods for taking measurements and analysis. Various techniques are used: induced fluorescence of chlorophyll, spectrophotometric and spectrometric (ICP) analyses, light and SEM microscopy, biochemical and molecular techniques combined with multivariate methods and the modelling of the adaptive response of plants to anthropogenic disturbances in ecosystems. Research results are used to assess the impact and consequences of the effects of anthropogenic habitat degradation on biodiversity and the functioning of the ecosystem. Besides its fundamental nature, this research is also applicative, aimed at restoration ecology. As such, different approaches and techniques are tested with the aim of defining an optimal model that will be effective in helping restore the biodiversity of different types of terrestrial ecosystems that have been disturbed to varying degrees.

Current phytoecological research is also focussed on studying forest populations, whose presence, genetic structure, and physiological, morphological and reproductive properties reveal the history of vegetation and the adaptive potential of local populations to survive in unfavourable environmental conditions. Research focuses on representative species of forest flora in protected ecosystems (in refugia, gorges, U-shaped valleys, and mountain ranges) and the most sensitive parts of ecosystems (on the edges of forest belts), as well as on discovering the migratory movement of species in the distant past and predicting patterns in the near future. Results of studying relict, endemic, endangered and economically significant (or potentially significant) forest species from our part of the Balkan peninsula provide a scientific basis for maintaining and protecting biodiversity and represent concrete support for the implementation of international obligations regarding protecting the biodiversity of forest ecosystems and endangered species.

With the aim of establishing the interactivity and interdependence of the geological substrate, soil, climate, biodiversity and local population, ethnobiological research that facilitates the assessment of the economic importance of natural habitats is undertaken. This research is aimed above all at preserving natural resources, and protecting ethnobotanical material and the biodiversity of regions.

Zooecological research is aimed at investigating the effects of abiotic (pollutants) and biotic (ecto- and endoparasites and microorganisms) factors on the immune system of mouse-like rodents which are sensitive to different influences from the external environment due to their high complexity. This research is carried out on the species Ratus norvegicus, which is considered a natural immunobiological model for investigating defence mechanisms. The impact of pollutants (cadmium) or rodenticides (warfarin) on the immune system of different breeds of laboratory and natural populations of R. norvegicus is examined through analyzing cellular and molecular mechanisms of immunomodulatory (proinflammatory and immunosuppressive) capacity under basal conditions of immune functions. In addition, research focuses on the induction of the immune response, particularly on the resistance to opportunistic microorganisms, such as the fungus Aspergillus fumigatus. Research into mechanisms of resistance to warfarin in natural populations of mouse-like rodents is undertaken through examining and analyzing the immunomodulatory potential of this rodenticide.

Zooecological research is also aimed at studying ornithofauna: determining the qualitative and quantitative components of populations of the ornithofauna of various habitats, determining the smallest area of habitat necessary for preserving communities of birds and home range endangered species, monitoring indicatory species or groups of species as part of the monitoring of natural habitat disturbance and global climate changes, distinguishing centres of biodiversity and linking them via corridors between fragmented habitats, census and demographic monitoring of endangered species of bird (primarily the vulture Gyps fulvus), the conservation of biodiversity, conservation ecology and the reintroduction of bird species that have disappeared to the Balkan peninsula, and establishing the monitoring of endangered and important species of ornithofauna.