This study examines the rates and patterns of molecular evolution in sister species separated by the Isthmus of Panama, focusing on the genus *Alpheus* snapping shrimp. The authors use allozymes and the mitochondrial COI gene to analyze 15 pairs of sister species, finding that genetic divergence varies fourfold among these pairs. Sister species from mangrove environments show the least divergence, suggesting they were among the last habitats to be divided. The estimated rate of sequence divergence is 1.4% per million years, implying separation times ranging from 3 to 18 million years ago. The study challenges the assumption that all sister species pairs diverged simultaneously around 3 million years ago, as suggested by past studies. The findings suggest that many past estimates of molecular evolution rates may have been overestimated due to the sampling of pairs that diverged before the final closure of the Isthmus. The authors discuss the implications of these results for calibrating molecular clocks and the broader applicability of their findings to other marine groups.This study examines the rates and patterns of molecular evolution in sister species separated by the Isthmus of Panama, focusing on the genus *Alpheus* snapping shrimp. The authors use allozymes and the mitochondrial COI gene to analyze 15 pairs of sister species, finding that genetic divergence varies fourfold among these pairs. Sister species from mangrove environments show the least divergence, suggesting they were among the last habitats to be divided. The estimated rate of sequence divergence is 1.4% per million years, implying separation times ranging from 3 to 18 million years ago. The study challenges the assumption that all sister species pairs diverged simultaneously around 3 million years ago, as suggested by past studies. The findings suggest that many past estimates of molecular evolution rates may have been overestimated due to the sampling of pairs that diverged before the final closure of the Isthmus. The authors discuss the implications of these results for calibrating molecular clocks and the broader applicability of their findings to other marine groups.