A consequence of introduction of alien species can be hybridization with a closely related native species. Hybridization can have a large effect on the genetic structure and conservation status of native populations. Here, we present a study of hybridization and introgression between native red deer (Cervus elaphus) and introduced sika deer (C. nippon) from 5 regions in Poland, the Kaliningrad District (Russia), and Lithuania. With a set of microsatellite loci and a mitochondrial marker, we uncovered extensive hybridization in all regions despite different population dynamics and no reports of hybrid individuals. We propose that sika populations in Eastern Europe were established with individuals coming from at least 2 different localities in southern Japan and eastern China. Legislation designed to reduce threats posed by sika deer could help to prevent further hybridization.