The Branchiopoda (Arthropoda: Crustacea) have traditionally been subdivided into four orders: Anostraca, Notostraca, Conchostraca, and Cladocera. The evolutionary relationships among the species of the Branchiopoda have occasionally been investigated by several authors. However they have failed to give any conclusive results about the phylogenetic relationships because of the extremely diverse morphological characters. Here molecular evolutionary study of the Branchiopoda was conducted by means of the nucleotide sequences of 18S ribosomal RNA of the six representative species including two reference species (Decapoda, Procambarus leonensis; Ostracoda, Cypridopsis sp.; Branchiopoda, Artemia salina of Anostraca, Daphnia sp. of Cladocera, Triops sp. of Notostraca, Lynceus gracilicornis of Conchostraca). Two kinds of aligned sets of nucleotide sequences were prepared: one with gaps and the other without gaps. Two kinds of methods were employed to construct the evolutionary tree: a distance matrix method and a maximum partimony method. d value (estimates of the number of nucleotide substitutions per site) and p value (proportion of different nucleotides) were calculated from the aligned set without gaps and UPGMA clustering method was used for constructing evolutionary tree as one of the distance matrix methods. The All tree options of the PAUP program package were applied to the two aligned sets of nucleotide sequences for the maximum partimony method. A related class Ostracoda was split off the Branchiopoda as expected. Within the groups of the Branchiopoda, Conchostraca is most closely allied to Notostraca in evolutionary trees resulting from the above two methods. The relationships of Anostraca and Cladocera with other groups remain to be solved through further study.