Hybridization of Drosophila homeo box DNA probes to Southern transfers of genomic DNA from the Hawaiian sea urchin Tripneustes gratilla has revealed that the sea urchin genome contains at least five homeo boxes. Examination of the DNA from several individuals shows that the sequences flanking these homeo boxes exhibit little restriction fragment length polymorphism, indicating they are more highly conserved than the majority of sea urchin DNA. Several clones in a T. gratilla genomic DNA library which hybridized with Drosophila homeo box probes were identified, and one found to be transcribed during embryogenesis was selected for further study. Southern transfer hybridizations showed the cloned gene to be single‐copy. DNA sequencing of the sea urchin gene defined a homeo box 70‐73% homologous to the Drosophila homeo box probes and an encoded homeo domain 78‐88% homologous to those encoded by the probes. Hybridization of DNA probes from the sea urchin homeo box‐containing gene to Northern transfers of embryonic RNA demonstrated that the gene produces two transcripts of 6.9 kb and 7.7 kb. Transcripts first accumulate at blastula stage and increase to a maximum level at gastrula stage before decreasing considerably in abundance by pluteus stage.