Identification of mechanisms that shape parasite community and metacommunity structures have important implications to host health, disease transmission, and the understanding of community assembly in general. Using a long-term dataset on parasites from desert rodents, we examined the relative contributions of host traits that represent important aspects of parasite environment, transmission probability between host species, and host phylogeny to the structure of a parasite metacommunity as well as for taxonomically restricted parasite metacommunities (coccidians, ectoparasites and helminths). This was done using a combination of metacommunity analysis and variance partitioning based on canonical correspondence analysis. Coccidian and ectoparasite metacommunities did not exhibit coherent structure. In contrast, helminths and the full parasite metacommunity had Clementsian and quasi-Clementsian structure, respectively, indicating that parasite species distributions for these metacommunities were compartmentalized along a dominant gradient. Variance decomposition indicated that characteristics associated with the host environment consistently explained more variation than did host traits associated with transmission opportunities or host phylogeny, indicating that the host environment is primary in shaping parasite species distributions among host species. Moreover, the importance of different types of host traits in structuring parasite metacommunities was consistent among taxonomic groups (i.e. full metacommunity, coccidians, and helminths) despite manifest differences in emergent structures (i.e. Clementsian, quasi-Clementsian, and random) that arose in response to variation in host environment.