This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Schistosomiasis is a severe debilitating illness that represents one of the most important parasitic diseases in tropical areas. It affects over 200 million people across 74 countries. The complete genome sequences of Schistosoma mansoni and Schistosoma japonicum were published in 2009, while some genomic data is available for Schistosoma haematobium, the most important parasite in the group, Beyond this, however, little is known about the diversity of schistosomes genome-wide, with only relatively limited micro-satellite data from relatively small panels of markers published to-date. We aim to expand our knowledge of schistosome diversity by sequencing additional strains of S. mansoni to get information about diversity at a relatively micro-evolutionary scale, and by sequencing additional species of schistosomes to get a broader view.