Sphox11/13b is one of the two hox genes of Strongylocentrotus purpuratus expressed in the embryo. Its dynamic pattern of expression begins during gastrulation, when the transcripts are transiently located in a ring of cells at the edge of the blastopore. After gastrulation, expression is restricted to the anus-hindgut region at the boundary between the ectoderm and the endoderm. The phenotype that results when translation of Sphox11/13b mRNA is knocked down by treatment with morpholino antisense oligonucleotides (MASO) suggests that this gene may be indirectly involved in cell adhesion functions as well as in the proper differentiation of the midgut-hindgut and midgut-foregut sphincters. The MASO experiments also reveal that Sphox11/13b negatively regulates several downstream endomesoderm genes. For some of these genes, Sphox11/13b function is required to restrict expression to the midgut by preventing ectopic expression in the hindgut. The evolutionary conservation of these functions indicates the general roles of posterior Hox genes in regulating cell-adhesion, as well as in spatial control of gene regulatory network subcircuits in the regionalizing gut.