Although we live in what is often touted as the 'post-genomic era', this term is hardly appropriate when we consider the paucity of knowledge of the genomic biology of parasitic flatworms. The situation is, however, changing-at least for two species of Schistosoma. Recent transcriptome analysis of Schistosoma mansoni and of Schistosoma japonicum has identified novel genes and genes not previously reported for schistosomes, as well as the identification of the molecular mechanisms for host-dependent maturation, immune evasion, development, signalling and sexual dimorphism. The analyses also identify potential vaccine candidates and drug targets. Here, the current state of knowledge is reviewed for mitochondrial and nuclear genomes of parasitic flatworms. We highlight the remarkable recent progress in gene discovery for schistosomes and the goal of sequencing complete schistosome genomes.