In the endoparasitic wasp Venturia canescens (Hymenoptera: Ichneumonidae) two genetically distinct lines, which differ at the VLP1 gene locus, appear to coexist sympatrically in thelytokous as well as arrhenotokous field and laboratory strains. Both lines display quite distinct morphological, physiological and behavioural variations, such as different oviposition strategies, egg numbers and growth rates during early embryonic development. To examine whether more than one gene is affected in the two lines, we applied cDNA-amplified fragment length polymorphism analysis to examine patterns of gene expression in ovaries of both wasp lines. We show that a number of ovarian transcripts have an altered expression pattern in either line, which was further confirmed by virtual Northern blot analysis. Sequence analysis of the cDNA-amplified fragment length polymorphism fragments revealed that some of the respective genes are expected to be involved in regulation of protein degradation during stress responses and in signal perception/transduction. The full-length sequence of two transcription factors (a homeodomain containing protein and a zinc finger protein) differentially expressed in both lines was obtained by RACE-polymerase chain reaction and their putative role in regulating key developmental processes during embryogenesis is discussed.