Molecular research of family Cervidae is new in Lithuania. There are multitude morphological and ecological studies, but so far no data on the genetic diversity of the deer in Lithuania, has been published. This dissertation presented genetic diversity studies of sika deer, red deer and roe deer and assessed the impact of non-native animal to community diversity and stability. The most important results of this study are the first time set of microsatellite markers were used to sika deer population genetic studies, which until now has been only used in research of reindeer, roe deer, fallow deer and red deer. Hybrid animals are found in sika deer and red deer populations (in nature and in captivity). We identified the 20 mtDNA D-loop sequence fragments of roe deer and placed in the \”GenBankâ€� sequence database (identification numbers:KM215767-KM215786). Three new haplotypes and eight mtDNA sequences in Lithuania roe deer population were unique and has no equivalent in \”GenBank\” deposited sequences. Results indicated introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, introgressed individuals constituted 20% of the roe deer studied.