The study of the factors that determine the structure and genetic diversity of natural populations is critical to understand their demographic and evolutionary trajectories and thus to predict their responses to future environmental changes (Freedman et al. 2010). In this thesis we have studied the genetic structure and the relationship between genetic diversity and fitness measured in terms of parasite prevalence, survival and development of ornaments in Mediterranean populations of blue tits (Cyanistes caeruleus). We used microsatellite markers classified as neutral and functional depending on whether they are located in regions of the genome that are actively transcribed RNA (Olano-Marín et al. 2011ab). The results of the genetic analysis showed some limitation to gene flow between the populations studied. The females had higher dispersion distances than males, a pattern that was reflected in the presence of genetic structure in males but not in females. Landscape genetic analyzes also revealed a genetic structure of populations, although it was subtle, possibly due to habitat fragmentation could force individuals to disperse greater distances through unfavorable habitats to reach new breeding sites (Wiens 2001; Harrison et al. 2013). Furthermore, the genetic structure was detected primarily to neutral markers, which could be because the functional markers were subject to selection stabilizer. The spatial heterogeneity and fragmentation of populations also seem to have generated differences in the prevalence of avian malaria between areas of study. The probability of infection with avian malaria was non-linear associated with heterozygosity estimated with neutral markers, so that individuals with intermediate levels of heterozygosity had higher probability of being parasitized (Blondel et al. 2009; Ruíz-López et al. 2012). This relationship was not significant for subset of functional markers, not differ between study areas with different degrees of parasitic pressure. However, the environmental context influence on direction and intensity of the relationship between genetic diversity and annual probability of survival. In particular, we observed that accumulated precipitation was positively correlated with the intensity of selection on heterozygosity. In addition, the selection of heterozygous individuals and moderate heritability of heterozygosity seem to have generated a gradual increase of genetic diversity in the population, suggesting a micro-evolutionary response to selection (Kaeuffer et al. 2007; Forcada & Hoffman2014). Finally, we observed a positive relationship between the expression of secondary sexual characters and heterozygosity estimated with functional markers on males. This indicates that the mechanism by which females select partner might be mediated by the increased capacity of males with high genetic diversity to develop ornaments, which could facilitate the election by the female of a couple with higher genetic quality (Candolín 2003). Overall, the results from this thesis highlights the importance of integrating different types of molecular markers and ecological data obtained at different space-time scales to improve understanding of the factors that determine the genetic structure of natural populations, as well as the consequences that genetic diversity has on different components of fitness.