Urbanization alters habitat structure and microclimatic conditions, potentially reshaping ectoparasite population dynamics. We investigated habitat-related variation in infestation patterns of pterygosomatid mites (Geckobia spp.) parasitizing the Moorish gecko Tarentola mauritanica in Morocco. Fifty-nine adult individuals (31 urban, 28 natural) were sampled between February and May 2024. Mite loads were quantified under stereomicroscopy. Prevalence was analyzed using binomial generalized linear models, while infestation intensity was modeled with negative binomial GLMs to account for parasite aggregation. Mite prevalence was consistently high in both habitats (100% in natural vs. 87.1% in urban populations) and did not differ significantly. In contrast, infestation intensity was markedly higher in natural habitats (39.5 ± 32.28 mites per host) compared to urban environments (6.26 ± 7.12). Habitat type was the strongest predictor of mite load, with additional effects of host sex and morphology; males exhibited higher infestation intensity. These results indicate that anthropogenic environments may constrain mite population growth or off-host survival without reducing transmission probability. The dissociation between prevalence and intensity highlights the importance of distinguishing infection occurrence from parasite aggregation in ecological acarology. This study provides one of the first quantitative assessments of pterygosomatid mite ecology in North Africa and emphasizes the sensitivity of host–mite systems to habitat transformation.