The achaete-scute (ac/sc) genes are a highly conserved family of transcription factors that play important roles in the development of neural cells in both vertebrates and invertebrates. As such, the study of arthropod ac/sc gene expression during neurogenesis has become a model system for investigating the evolution of neural patterning. To date, ac/sc gene expression has been investigated in insects, chelicerates, and myriapods. Here we present the identification of two ac/sc genes from the branchiopod crustacean Triops longicaudatus. Triops longicaudatus achaete-scute homologs1 and 2 (Tl-ASH1 and Tl-ASH2) exhibit dynamic and distinct expression profiles during Triops neurogenesis. Tl-ASH1 expression initiates in nearly all cells of the neurogenic region and subsequently in clusters of cells evenly spaced along the length of the developing limbs. In contrast, Tl-ASH2 initiates expression after Tl-ASH1. In the CNS, only a subset of Tl-ASH1 cells appears to express Tl-ASH2. Similarly, in the PNS individual Tl-ASH2 positive cells appear to arise from the clusters of Tl-ASH1 expressing cells. Shortly after activating Tl-ASH2 expression, these cells enlarge and divide. The expression dynamics of ac/sc genes in Triops parallel those observed in insects and contrasts with those found in chelicerates and myriapods.