The marine faunas of tropical America underwent substantial evolutionary turnover in the past 3 to 4 million years in response to changing environmental conditions associated with the rise of the Isthmus of Panama, but the ecological signature of changes within major clades is still poorly understood. Here we analyze the paleoecology of faunal turnover within the family Pectinidae (scallops) over the past 12 Myr. The fossil record for the southwest Caribbean (SWC) is remarkably complete over this interval. Diversity increased from a low of 12 species ca. 10–9 Ma to a maximum of 38 species between 4 and3 Ma and then declined to 22 species today. In contrast, there are large gaps in the record from the tropical eastern Pacific (TEP) and diversity remained low throughout the past 10 Myr. Both origination and extinction rates in the SWC peaked between 4 and 3 Ma, and remained high until 2–1 Ma, resulting in a 95% species level turnover between 3.5 and 2 Ma. The TEP record was too incomplete for meaningful estimates of origination and extinction rates. All living species within the SWC originated within the last 4 Myr, as evidenced by a sudden jump in Lyellian percentages per faunule from nearly zero up to 100% during this same interval. However, faunules with Lyellian percentages near zero occurred until 1.8 Ma, so that geographic distributions were extraordinarily heterogeneous until final extinction occurred. There were also striking differences in comparative diversity and abundance among major ecological groups of scallops. Free-swimming scallops constituted the most diverse guild throughout most of the last 10 Myr in the SWC, and were always moderately to very abundant. Leptopecten and Argopecten were also highly diverse throughout the late Miocene and early Pliocene, but declined to very few species thereafter. In contrast, byssally attaching scallops gradually increased in both diversity and abundance since their first appearance in our samples from 8–9 Ma and are the most diverse group today. Evolutionary turnover of scallops in the SWC was correlated with strong ecological reorganization of benthic communities that occurred in response to declining productivity and increased development of corals reefs.