Analysis of trematode parasite communities in fish eye lenses by pyrosequencing of naturally pooled DNA

► We used pyrosequencing to quantify interspecific SNPs in pooled parasite samples. ► The method represents a valuable tool for analyzing parasite communities as a whole. ► We investigated communities of eye flukes in lenses of freshwater fish. ► Communities differed among fish species and multiple species infections were common. ► The method can be used in evolutionary ecology studies of host-parasite interactions.