It has long been known that the asymmetry of snails, including the direction of shell coiling, is determined by the delayed effect of a maternal gene on the chiral twist that takes place during early embryonic development. Yet, the identity of the gene and the means by which left-right asymmetry is established in snails remains unknown. To put in place the resources for identification of the chirality gene (“D”), heterozygous (Dd) pond snails Lymnaea stagnalis were self-fertilised or backcrossed, and the genotype inferred of more than six thousand offspring, either dextral (DD/Dd) or sinistral (dd). Twenty of the offspring were used with Restriction-site-Associated DNA Sequencing (RAD-Seq) to identify anonymous molecular markers that are putatively linked to the chirality locus. A local genetic map was constructed following the genotyping of three markers in a more than three thousand snails. The three markers flank either side of the chirality locus, with one very tightly linked (<0.1 cM). Subsequently, bacterial artificial chromosomes (BACs) were isolated that contain the three loci. Fluorescent in situ hybridization (FISH) of pachytene cells showed that the three loci tightly cluster on the same bivalent chromosome. Fibre-FISH confirmed that the chirality locus is contained between the two of the BACs, within a physical distance of around ~400 kb or greater. This work therefore sets in place the resources for identification of the gene itself. More generally, the results also show that high resolution FISH is a robust technique for physical mapping in snails, and so may be useful in assembling repetitive molluscan genomes.