Transposable elements are important factors to cause genetic variation and recombination, which are widely spread in eukaryotic organisms. Object to the increasing numbers of transposable elements in protozoa genome, this review focus on the types and genomic distributions of transposable elements in newly completed genome of protozoa parasite, mainly including Trypanosoma, Leishmania, microsporidia, Amoebozoa. The LINE and SINE elements are predominated in protozoa genome, followed by the DNA transposons and LTR retrotransposons. Several elements incline to insert in AT-rich region, suggesting the possible close relationship between the activity of transposable elements and AT content of genome. By the comparison of the divergence of transposable elements in microspordian genome, it was hypothesized that at least one loss event of transposable element had occurred during microsporidian genomic evolution. Finally, the prospects of trans-posable elements were discussed in the application of functional gene research of protozoa.