Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. Here, eDNA is defined as the genetic material obtained from a water sample containing no distinguishing characters of original macroorganisms. Potential sources of eDNA are all the biomaterials of organisms. Degradation of eDNA depends on different abiotic conditions. eDNA analysis is of great importance in research and determination of environmental biodiversity because it is a simple and cost-effective method that also enables quantitative assessment of biomass and abundance of individuals and species. Changes in environment reflect in environmental DNA and therefore the eDNA analysis is often used in ecology. Besides climate change there are also seasonal changes of abiotic factors that significantly affect degradation of eDNA. The Mediterranean is a hotspot of biodiversity, researched using traditional and modern methods. In modern times this biodiversity is threatened by non-indigenous species whose monitoring is facilitated with environmental DNA analysis.