The presence or absence of parasites within host populations is the result of a complex of factors, both biotic and abiotic. This study uses a non-parametric classification tree approach to evaluate the relative importance of key abiotic and biotic drivers controlling the presence/absence of parasites with complex life cycles in a sentinel, the common killifish Fundulus heteroclitus. Parasite communities were classified from 480 individuals representing 15 fish from 4 distinct marsh sites in each of 4 consecutive seasons between 2006 and 2007. Abiotic parameters were recorded at continuous water monitoring stations located at each of the 4 sites. Classification trees identified the presence of benthic invertebrate species (Gammarus sp. and Littorina sp.) as the most important variables in determining parasite presence: secondary splitters were dominated by abiotic variables including conductance, pH and temperature. Seventy percent of hosts were successfully classified into the correct category (infected/uninfected) based on only these criteria. The presence of competent definitive hosts was not considered to be an important explanatory variable. These data suggest that the most important determinant of the presence of these parasite populations in the common killifish is the availability of diverse communities of benthic invertebrates.