Factors constraining host specificity are poorly understood. Intraspecific variation in host preferences in generalist parasites may reveal which factors affect patterns of host use, and thus the evolution of specialization. Here, laboratory experiments examined genetic variation in host preferences and the effect of a refugium against infection on host use. Firstly, 6 cercarial clones of the trematode Maritrema novaezealandensis (ranging widely in heterozygosities) were exposed simultaneously to 2 alternative hosts, the amphipods Heterophoxus stephenseni and Paracalliope novizealandiae, to assess host preferences and fitness correlations with parasite heterozygosity. All clones showed a distinct preference for H. stephenseni, though the extent of this preference varied among clones. No clear association was found between heterozygosity and either parasite infection success or preference for a particular host. Secondly, cercariae were exposed to the same 2 amphipods in both the presence and absence of sand (r