Two Drosophila receptor-like tyrosine phosphatase genes, DPTP99A and DPTP10D, were characterized. Protein products of these genes show distinct expression patterns specific to subsets of developing CNS axons. DPTP99A expression coincides with the onset of axonogenesis and is expressed in several pioneer neurons, including aCC and RP2, which pioneer the intersegmental nerve; its proteins are transiently expressed in the intersegmental and segmental nerves, arguing for a role in the establishment of these nerves. Both genes produce complex sets of transcripts, owing to the alternative utilization of exons and polyadenylation sites. Each gene produces alternative protein forms, which differ in their C-terminal tails. The deduced proteins possess extracellular FN-III repeats and intracellular PTPase domain(s). We discuss the implications of these results and the role of protein tyrosine dephosphorylation in axon outgrowth and guidance.