The PPM has been recently recognized as a possible model species to study the consequences of global warming. This is notably due to the recent discovery of a population exhibiting a shifting phenology, the summer population (SP) that coexists in sympatry with a traditional winter population (WP) in the forest of Leiria in Portugal. A candidate gene approach is undertaken to look for genetic changes associated with this differential phenology. The rangewide genetic structure from two biological clock candidate genes is described, and compared with data from mitochondrial maker. It has been demonstrated that the newly emerged SP originated from the local SP population, but none of the genes sequenced during the course of our study allows to differentiate them. However, they prove to be useful to give new enlightenments on the phylogeny of the species.