The molecular phylogeny of economically important shrimp species of Taiwan was revealed by partial mitochondrial 16S rRNA sequences amplified from 20 species (belonging to five families) in this study. Alignment of the sequences showed considerable variation in 209 nucleotide sites and 154 parsimoniously informative sites. Phylogenetic trees were created by Neighbor-joining and maximum parsimony methods. We determined that (1) the family Solenoceridae is included within the Penaeoidae, and it seems to be more suitable to be classified in the tribe Peneini than the tribe Parapeneini of the family Penaeidae; (2) the family Penaeoidae appeared to have a paraphyletic status that formed at least three clades which support the opinion of Burkenroad from morphological studies and previous molecular studies; and (3) the species Metapenaeus ensis was shown to form a clade by itself, which clearly indicates that M. ensis is outside the tribe Trachypeneini.