Understanding how host dynamics, including spatiotemporal variations of population size and dispersal, may affect the epidemiology of infectious diseases is an active research area. Population dynamics drive neutral and adaptive micro-evolutionary processes that in turn, influence pathogens persistence, their distribution and evolution. This study focuses on a bank vole (Myodes glareolus) metapopulation surveyed in Finland between 2005 and 2009. Bank vole is the reservoir of Puumala hantavirus (PUUV), the agent of nephropathia epidemica (NE, a mild form of hemorrhagic fever with renal symptom) in humans. M glareolus populations experience multiannual density fluctuations that influence the level of genetic diversity maintained in bank voles, variations in PUUV prevalence and NE occurrence in humans. Here, we examine bank vole metapopulation genetics at presumably neutral markers and immune-related genes (Tnf-promoter, Mhc-Drb, Tlr4, Tlr7 and Mx2 gene). We discuss its potential consequences on PUUV epidemiology. Using microsatellites, we show that genetic drift slightly and transiently affects neutral and adaptive genetic variability within the metapopulation. Gene flow seems to counterbalance its effects during the multiannual density fluctuations. The low abundance phase may therefore be too short to impact genetic variation in the host, and consequently viral genetic diversity. Environmental heterogeneity does not seem to affect vole gene flow, which might explain the absence of spatial structure previously detected in PUUV in this area. We find evidence for the role of vole dispersal on PUUV circulation through sex-specific and density-dependent movements. We also analyze how density cycles affect selection acting on immune-related genes involved in susceptibility to PUUV. We detect associations between Mhc-Drb haplotypes and PUUV serology, and between Mx2 genotype and PUUV genogroups. We also find footprint of positive selection at Tlr-4 gene in 2008 only. These results emphasize the potential interactions between bank vole immunogenetics and PUUV microevolution.