Genetic differences that accumulate between species can result from the action of either random genetic drift or natural selection. However, the relative importance of drift vs. selection in causing the differences observed between species remains poorly understood. This study will used closely related species of Strongylocentrotid sea urchins to address several fundamental questions in the field of evolutionary genetics. First, what proportion of the genetic changes observed between species has been caused by natural selection? Second, have the selected changes occurred recently within existing species or do they reflect adaptation occurring further back in time? Third, what are the specific DNA regions that show evidence of past natural selection and can these changes be explained by known biological processes (such as reproduction or disease resistance)? The complete genome sequences from eight species of sea urchin were used to investigate these questions. The results provide new insights into the importance of selection as a force for genome evolution.