Schistosomiasis is a chronic and debilitating disease caused by blood flukes (digenetic trematodes) of the genus Schistosoma. Schistosomiasis japonica, a zoonosis caused by Schistosoma japonicum, is endemic to the Philippines and China. We utilised a 22,575 feature custom oligonucleotide DNA microarray designed from public domain databases of schistosome-expressed sequence tags to explore differential gene expression between the Philippine (SJP) and Chinese (SJC) strains of S. japonicum, and between male and female S. japonicum. We found that 593, 664 and 426 probes were differentially expressed between the two geographical strains when we compared mix sexed adults, male worms and female worms. Additionally, the study revealed that 1163 male- and 1016 female-associated probes were differentially expressed in SJP whereas 1047 male- and 897 female-associated probes were differentially expressed in SJC. The study greatly expands previously published data of strain and gender-associated differential expression in S. japonicum. Further, these new data provide a stepping stone for understanding the complexities of the biology, sexual differentiation, maturation, and development of human schistosomes, signaling new approaches for identifying novel intervention and diagnostic targets against schistosomiasis.