Parasite infestations depend on multiple host‐related and environmental factors. In the case of ectoparasites, which are exposed to the environment beyond the host, an impact of climate, expressed by seasonal or yearly variations, can be expected. However, long‐term dynamics of ectoparasite infestations are rarely studied in nonhuman primates. We investigated the yearly variations in ectoparasite infestations of two small primates, the gray (Microcebus murinus) and the golden‐brown (Microcebus ravelobensis) mouse lemur. For a more comprehensive evaluation, we also analyzed the potential effects of yearly and monthly climatic variation (temperature, rainfall) in addition to habitat, host sex, age, species, and body mass, on ectoparasite infestation. Individuals of both host species were sampled in two study sites within the Ankarafantsika National Park in northwestern Madagascar during several months (March–November) and across 4 years (2010, 2011, 2015, 2016). Our results show significant monthly and yearly variations in the infestation rates of three native ectoparasite taxa (Haemaphysalis spp. ticks, Schoutedenichia microcebi chigger mites, Lemurpediculus spp. sucking lice) and in ectoparasite species richness in both mouse lemur species. In addition, significant impacts of several host‐related (species, sex, body mass) and environmental factors (habitat, temperature, rainfall) were found, but with differences in relevance for the different parasite taxa and partly deviating in their direction. Although some differences could be attributed to either permanent or temporary presence of the parasites on the host or to ecological differences between the host species, the lack of specific knowledge regarding the life cycle and microhabitat requirements of each parasite taxon precludes a complete understanding of the factors that determine their infestation dynamics. This study demonstrates the presence of yearly and monthly dynamics in lemur–parasite interactions in tropical, seasonal, dry deciduous forests in Madagascar, which call out for broad ecological long‐term studies focusing both on primate hosts and their parasites.