Selection on parasites should favor adaptations that maximize the probability of transmission to the definitive host, such as the preference for and use of intermediate hosts or encystment substrata that are likely to be consumed by the definitive host. Eye flukes in the genus Philophthalmus are passed to their definitive avian host through the ingestion of metacercariae encysted on hard substrata. The life cycle of these parasites is generally well understood; however, there is almost no information on substratum use or preference of the cercariae of these parasites. In this study, we combine a survey of naturally occurring substrata with experimental, laboratory-based choice tests to determine the preferred substratum of Philophthalmus sp. and whether this preference is affected by the presence and density of pre-existing cysts. A concordance between natural and experimental data show a preference for the shells of multiple species of snail over other hard substrata that are common at the field site, including seaweed, other molluscs, and crustaceans. In addition, we found that cercariae preferred substrata with pre-existing cysts and that this preference seemed to increase with increasing cyst density. Such a preference should lead to an aggregated distribution of cysts among snail shells that may benefit the parasite by increasing the number of potential mates that become established in the definitive host. The identification of a preferred substratum also may help to identify potential definitive hosts that were previously unknown.