Host inflammatory responses directed against eggs laid by sexually-mature Schistosoma japonicum female worms instigate lesion formation and associated clinical pathologies during infection. To identify parasite gene transcripts that associate with egg production and to characterise sexually-mature adult gene expression profiles of two related Chinese strains, S. japonicum cDNA microarrays were fabricated using 457 ESTs originating from three parasite developmental stages. Twenty-two female-associated and 8 male-associated gene transcripts were identified in the adult Anhui strain whereas 21 female-associated and 7 male-associated gene transcripts were revealed in the adult Zhejiang strain. RT-PCR analysis, in situ enzyme localisation studies and enzymatic assays confirmed the cDNA microarray results, and importantly, provided information previously unappreciated in schistosome conjugal biology. Specifically, our novel findings include the female-specific expression of genes putatively involved in haemoglobin digestion and eggshell formation including extracellular superoxide dismutase, two histidine-rich proteins, a large blood-brain barrier amino acid transporter and two tyrosinase orthologues. In contrast, transcripts involved in mechanical support (actin), cytoskeletal infrastructure (e.g. dynein light chain 3 and myosin regulatory light chain) and tegumental biology (e.g. TM4SF and Sj25) were more highly represented in adult male schistosomes. Together these data establish a transcriptional basis for adult schistosome labour division and expands the list of novel S. japonicum gender-associated gene transcripts that may be considered targets for improved intervention strategies.