By comparing the spatial and temporal distribution of three proteins during early development in seven echinoid species, we demonstrate that both heterochronies and heterotopies in gene-product expression have accompanied the radiation of post-Paleozoic echinoids. All three proteins examined showed significant alterations in time of expression, site of expression, or both. These molecular heterochronies and heterotopies indicate that early development is not necessarily as evolutionarily conservative as morphology of embryos alone would suggest. Evolutionary alterations in early development may be more common than is generally assumed.