Understanding how habitat type and deterioration may affect parasitism is important in assessing the effects of human-induced environmental change on host–parasite dynamics. In this study, we examined inter-population differences in parasite load in the Mediterranean lizard Psammodromus algirus (Linnaeus, 1758). We analyzed prevalence and intensity of infection by blood parasites and ectoparasites in two populations separated by a 400 m elevational gradient and with different habitat types that also differed in the degree of human alteration. We also compared data obtained from the same populations 10 years later to assess whether there have been temporary changes in parasite loads. Results showed that prevalence and intensity of blood parasites were higher in the deteriorated lowland holm oak forest population than in the well-preserved upland oak forest. In contrast, the prevalence and intensity of infection by Ixodes Latreille, 1795 ticks was higher in the upland oak forest population. Individuals from the lowland population were in poorer condition. Intensities of infection by blood parasites and ectoparasites have decreased significantly from 2005–2006 to 2016 in both populations. Our results suggest that inter-population differences in parasite load may be explained by differences in habitat characteristics. This study contributes to the identification of ecosystems and habitats that are most sensitive to prevalence and intensity of infection by parasites.