The secondary mesenchyme cells (SMCs) give rise to most of the mesoderm of the sea urchin embryo. Although the early embryonic lineage of these cells has been described, the mechanisms that cause SMCs to become restricted to a particular mesodermal cell fate are unknown. To begin to address this question, we performed a clonal analysis of the fates of SMC precursors in the vegetal plate by labeling single cells with the fluorescent dye DiI (C18). Our data show that some presumptive SMCs remain pluripotent at the late blastula stage, since some cells labeled at this stage gave rise to more than one mesodermal cell type. Surprisingly, however, most labeled cells gave rise to homogeneous clones composed of a single cell type. This observation indicates that either many SMC precursors are restricted in their fate before the start of gastrulation or that all the progeny of a single vegetal plate cell are influenced by the same instructional signals during gastrulation, despite the cell divisions and extensive cell movements that occur during this time. The percentage of clones composed of a single cell type increased during the blastula stage, supporting the view that the process of SMC fate specification begins before the onset of gastrulation.