The establishment of in vitro cultivation techniques to maintain larval and adult stages of the trematode Schistosoma mansoni has facilitated research on diverse aspects of the biology of this parasite. Because of the difficulty in obtaining defined intramolluscan stages of this parasite, one aim of this study was to develop an in vitro technique for the generation of defined clonal daughter sporocyst (DSp) generations that originate from a single mother sporocyst. Sporocysts died when cultured singly; however, when single sporocysts were cultured in inserts within wells with about 1,000 others, the single individuals produced daughters asexually. In recent years, evidence has been accumulating for variability among, and within, schistosome populations. Such variability has been seen in both larval and adult stages. Even within clonal cercariae, genomic and biochemical heterogeneity has been observed, indicating the existence of a yet unknown mechanism that generates variability during larval development. Therefore, another aim of this study was to examine clonal DSps generated in vitro for diversity regarding the presence or absence of a specific repetitive DNA element (W1). Such sporocysts were found by molecular analysis to be heterogeneous with respect to the occurrence of W1. This phenomenon had previously been observed in clonal schistosome populations and described as genomic instability. In this study, we provide the first molecular evidence that variability can be generated within sporocyst generations, supporting the hypothesis of mitotic recombination events during the asexual life stage of schistosomes.