Monitoring individuals and their abundance has become an important tool for species management and conservation. Genetic monitoring of species gives insights into the genetic composition of individuals and populations, but also allows to identify individual movement and to assess sex ratios and population sizes, and changes thereof, in a spatio-temporal framework. For elusive and difficult-to-spot animals, noninvasive methods have emerged as a valuable approach, as they do not require handling or seeing individuals. Hereby, remnants of individuals (e.g. feces) are collected in the field and used as source of genetic material. Here, we present the five-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in the Swiss National Park. We used genetic fingerprinting and a sex marker to identify individuals from feces samples. We found that females showed higher apparent survival than males. Male abundance in the area showed high seasonal fluctuations, mostly due to seasonal changes of apparent survival rates. Generally, males and females showed only little temporary movement into and out of the study area. Additionally, through including reference genotypes of European hares (Lepus europaeus), we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2300 m a.s.l. in the spring of 2016. Further, we found signs of hybridization between the two species. For elusive animals, such as mountain and European hares, the here presented methods provide valuable insights into population size changes. For future monitoring studies of mountain hare, we suggest including highly resolving markers to identify species and individuals to assess the potential threats to mountain hare given through competitive exclusion by and hybridization with the European hare.