Abstract In this study we document the prevalence of gastrointestinal parasites (helminths and protozoans) found in fecal samples of populations of Alouatta palliata mexicana and of A. pigra in Los Tuxtlas and in Palenque, southeast Mexico, and its relation to habitat condition, sex/age and season. Nineteen parasite morphotypes were detected in the fecal samples from populations of the two howler monkeys, of which 58% were shared by both species. When considering all parasite species, populations of the two howler species were more likely to be parasitized in fragmented habitat compared to continuous habitat. Individuals of both howler monkey species that lived in fragmented habitat had a higher prevalence of Controrchis biliophilus. A. p. mexicana individuals had a higher prevalence of Trypanoxyuris minutus than A. pigra, probably the result of the larger group sizes found in the former species, and T. minutus was more likely to be found in A. palliata individuals that lived in fragmented habitat. Adult A. p. mexicana males had a higher risk of being parasitized compared to adult females, but these differences were not detected in A. pigra. Parasite species such as Entamoeba sp., Nematoda sp. 28, Nematoda sp. B and Parabronema sp. where only found during the wet season in both howler monkey species. Populations of both howler monkey species had a higher prevalence of Nematoda sp. A in the wet season and Ascaridae eggs were only detected during the wet season in A. pigra. Other parasites detected displayed no clear seasonal pattern.