The Isthmus of Panama has long been used as a model for estimating molecular evolution rates, based on the assumption that most species pairs separated by the isthmus diverged around 3 million years ago. However, this study challenges that assumption by analyzing 15 pairs of snapping shrimp in the genus Alpheus, which show varying degrees of genetic divergence. The results indicate that divergence times for these pairs range from 3 to 18 million years ago, with the most recent divergences occurring in mangrove habitats. The study finds that the rate of sequence divergence is 1.4% per million years, suggesting that earlier estimates may have overestimated molecular evolution rates. The findings highlight the importance of using multiple genetic markers and considering ecological factors when estimating divergence times. The study also suggests that some divergence events may have occurred before the final closure of the isthmus, and that non-simultaneous divergence is a common phenomenon. The results have implications for understanding molecular clocks and the biogeographic history of marine species. The study emphasizes the need for more comprehensive sampling of transisthmian pairs to accurately estimate molecular evolution rates.The Isthmus of Panama has long been used as a model for estimating molecular evolution rates, based on the assumption that most species pairs separated by the isthmus diverged around 3 million years ago. However, this study challenges that assumption by analyzing 15 pairs of snapping shrimp in the genus Alpheus, which show varying degrees of genetic divergence. The results indicate that divergence times for these pairs range from 3 to 18 million years ago, with the most recent divergences occurring in mangrove habitats. The study finds that the rate of sequence divergence is 1.4% per million years, suggesting that earlier estimates may have overestimated molecular evolution rates. The findings highlight the importance of using multiple genetic markers and considering ecological factors when estimating divergence times. The study also suggests that some divergence events may have occurred before the final closure of the isthmus, and that non-simultaneous divergence is a common phenomenon. The results have implications for understanding molecular clocks and the biogeographic history of marine species. The study emphasizes the need for more comprehensive sampling of transisthmian pairs to accurately estimate molecular evolution rates.