Pinworms are nuisance parasites of man and animals. In addition to the human pinworm Enterobius vermicularis, Syphacia muris has been reported to infect man. Morphological differences between pinworm species are difficult to determine. Polymerase chain reaction (PCR) based assays including random amplified polymorphic DNA (RAPD) have been used effectively as a complementary approach for fast and simple detection of genomic variability and similarity among parasites. Such information is essential for accurate identification and for finding appropriate experimental models for species under study.