Fecal samples from captive and free-living lemurs at Ivoloina Zoological Park (IZP) and domestic carnivores from six villages surrounding IZP were evaluated between July and August 2012. Free-living lemurs from Betampona Natural Reserve (BNR), a relatively pristine rainforest fragment 40 km away, were also evaluated in November 2013. All 33 dogs sampled (100%) and 16 of 22 cats sampled (72.7%) were parasitized, predominantly with nematodes (strongyles, ascarids, and spirurids) as well as cestodes and protozoans. Similar types of parasites were identified in the lemur populations. Identification of spirurid nematodes and protozoans in the lemur fecal samples were of concern due to previously documented morbidity and mortality in lemurs from these parasitic agents. Twelve of 13 free-living (93%) and 31 of 49 captive (63%) lemurs sampled at IZP had a higher parasite prevalence than lemurs at BNR, with 13 of 24 (54%) being parasitized. The lemurs in BNR are likely at risk of increased exposure to these parasites and, therefore, increased morbidity and mortality, as humans and their domestic animals are encroaching on this natural area.