Intra- and inter-specific variation in ectoparasite prevalence was characterized by collecting and identifying parasites on Myotis septentrionalis (Northern Long-eared Bat) and Myotis lucifugus (Little Brown Bat) returning to a large hibernaculum during the autumn migratory and reproductive swarming event in Nova Scotia, Canada. Unlike males, female bats in the region are colonial roosters during the summer, which may facilitate ectoparasite transfer. On bats captured at Hayes Cave, NS, there were at least four species of ectoparasites including Myodopsylla insignis (Siphonaptera: Ischnopsyllidae), Spinturnix americanus (Acarina: Spinturnicidae), Cimex adjunctus (Hemiptera: Cimicidae), and a larval Trombiculid mite, Leptotrombidium myotis (Acarina: Trombiculidae). Parasite prevalence was 30.6% and 27.8% for adult M. septentrionalis females and males, respectively, and 25.6% and 16.3% for adult female and male M. lucifugus, respectively. Myodopsylla insignis, S. americanus, C. adjunctus, and L. myotis all represent new host records on both bat species in Nova Scotia, while S. americanus and L. myotis are new species records for the province.