The nematodes, Trichuris suis and Trichuris trichiura are believed to be two separate but closely related species. The aim of our study was to examine the morphological and genetic diversity of Trichuris spp. recovered from pigs and humans. Sympatric worm material isolated from 10 humans and 5 pigs in Uganda supplemented with T. suis from Tanzania, Denmark and USA and T. trichiura from England, was obtained. Based on morphology, worms from the two hosts could only be discriminated by the length of the male spicule (t-test, p<0.001). The second internal transcribed spacer (ITS-2) in the r-DNA was amplified by PCR and cloned. Between 1 and 6 clones from 20 worm were sequenced, which resulted in 49 human-derived and 45 pig-derived sequences that could be allocated into as many as 56 different haplotypes. A very large intra-individual variation was found within the human-derived sequences (0.2 – 45.0%) compared to the pig derived sequences (0.2 – 1.4%). This was due to the fact that the human-derived worms consisted of two main ITS-2 sequence types; one of them being unique (69% of the human-derived sequences, consensus sequence 481 nucleotides long) and the other being identical to the sequence type found in pig-derived worms (31% of the human-derived worms, consensus sequence 531 nucleotides long). The results indicated that the nematodes found in pigs belong to a genetically distinct species (T. suis) whereas the nematodes in humans showed considerable genetic variability either related to ancestral polymorphism or more recent cross-breeding between T. trichiura and T. suis.