The population of the Eurasian lynx (Lynx lynx) in the Czech Republic occurs on the edge of the species distribution in the Western Carpathians. The population is threatened by many factors such as habitat fragmentation, migration barriers and poaching. Status of the population in the transboundary area of the Czech and Slovak Republics was investigated on the basis of genetic material (scat, hair and urine samples ) collected in years 2010–2013 during snow-tracking sessions. Using in total 19 microsatellite loci and the sex specific marker SRY we identified 18 individuals of lynx. Our aim was to describe genetic variability and structure of population, population size using capture-mark-recapture model, effective population size, kinship and spatial distribution. We also compared these results with data from the parallel camera traps survey and snow-tracking. We discuss the key factors important for the lynx conservation in the Central Europe as a basis of a trans-boundary management plan for Eurasian lynx.