The microflora (microbes) of the gastrointestinal tract have been found to play an important role in the health of animals. In addition to pathogenic microbes and their associated negative effects, beneficial microbes have important positive effects. However, the dynamics of the transmission and colonization of the microflora between mates and between parents and offspring are still largely unknown. Variation in the microflora between individuals suggests that selection can play a role in this transmission and colonization. As a preliminary step to investigate the transfer of microflora between male and female isopods, microbial DNA from Oniscus asellus, washed and unwashed gastrointestinal tracts and hepatopancreas glands were isolated and characterized using 16S rRNA primers and DGGE analysis. Males and females showed considerable variation between microflora in gastrointestinal tracts while hepatopancreas samples were more similar.