Gene mapping and the generation of linkage groups are fundamental to an understanding of the organization and relationships of genes and marker sequences, providing a framework with which to investigate their association with traits of interest. The abundance of techniques available for generating polymorphic molecular markers, and recent advances in high throughput screening, have allowed the extension of map analysis to the tropical freshwater snail Biomphalaria glabrata, an important intermediate host for Schistosoma mansoni. Direct comparison of gene expression by differential display screening, without prior identification of candidate genes, can be combined with mapping to quantify the involvement of specific sequences in the schistosome resistance response, and other important host–parasite interactions. Here we discuss the application of current and emergent technologies to gene characterization and linkage analysis in snail–schistosome interactions. Preliminary results from the analysis of comparative gene expression in resistant and susceptible snails are also presented.