In the Daphnia magna–Pasteuria ramosa host–parasite system, the most important step of the infection process is the one in which P. ramosa spores attach to the host’s foregut. Here we describe a new parasite genotype, which, unlike previously studied genotypes, attaches to the host’s hindgut, not to its foregut. Host resistance shows great diversity across natural populations. Using a QTL approach, we detected one QTL that co-localizes with the previously described locus of resistance to foregut attachment, and a second, major QTL located in an unlinked genomic region. We find no evidence of epistasis.