Captive management practices have the potential to drastically alter pre-existing host-parasite relationships. This can have profound implications for the health and productivity of threatened species in captivity, even in the absence of clinical symptoms of disease. Maximising the success of captive breeding programmes requires a detailed knowledge of anthropogenic influences on the structure of parasite assemblages in captive systems. In this study, we employed two high-throughput molecular techniques to characterise the parasitic nematode (suborder Strongylida) communities of the red kangaroo, Macropus rufus, across seven captive sites. The first was terminal restriction fragment length polymorphism (T-RFLP) analysis of a region of rDNA encompassing the internal transcribed spacers 1 (ITS1), the 5.8S rRNA gene and the internal transcribed spacer 2 (ITS2). The second was Illumina MiSeq next-generation sequencing of the ITS2 region. The prevalence, intensity of infection, taxonomic composition and comparative structure of strongylid nematode assemblages was assessed at each location. Prevalence (P = <0.001) and mean infection intensity (df = 6, F = 17.494, P = <0.001) differed significantly between the seven captive sites. Significant levels of parasite community structure were observed (ANOSIM, P = 0.01), with most of the variation being distributed within, rather than between, captive sites. The range of nematode taxa that occurred in captive red kangaroos appeared to differ from that of wild conspecifics, with representatives of the genus Cloacina, a dominant nematode parasite of the macropodid forestomach, being detected at only two of the seven study sites. This study also provides the first evidence for the presence of the genus Trichostrongylus in a macropodid marsupial. Our results demonstrate that contemporary species management practices may exert a profound influence on the structure of parasite communities in captive systems.