Penaeid shrimp species are an important fisheries and aquaculture resource in tropical and subtropical shallow seas. Along the Brazilian coast the four most exploited, native species are Farfantepenaeus subtilis, F. paulensis, F. brasiliensis and Litopenaeus schmitti. Genetic knowledge on Penaeid species is growing but many basic systematic and population issues remain to be assessed. In the present work, DNA-based molecular tools were used to approach phylogenetic and population genetics questions concerning the Brazilian penaeids. Partial sequences for the 16S rRNA and Cytochrome Oxidase I (COI) mitochondrial genes were obtained from 11 penaeid shrimp species from the Western Atlantic and Eastern Pacific, and from an undescribed morphotype of pink shrimp usually identified as F. subtilis. The phylogeny resulting from the 16S and COI partial sequences showed that American Farfantepenaeus and Litopenaeus from two well-supported monophyletic clades in agreement with the two genera proposed in a recent systematic review of the suborder Dendrobranchiata. Consistent differences observed in the sequences from the F. subtilis morphotype, coupled with previous allozyme data, support the conclusion that this is a previously undescribed species of Farfantepenaeus. The genes of the nuclear ribosomal cluster were also partially or entirely sequenced for 11 species of American Penaeus. Both 18S and 5.8S genes were found to be highly conservative (average p=0.0028 and p=0.0000 respectively), whilst ITS1 sequences show strong evidence of intragenomic variability, in many cases resulting from the presence of microsatellite arrays inside the spacer. Despite that, distance based neighbor-joining trees support the 16S-COI phylogeny, and provide further evidence for the close genetic relationship between F sp and F. subtilis, in contrast to previous allozyme data that suggested a closer relationship between F sp and F. paulensis.