Four hundred years of commercial harvest of the oyster Pinctada mazatlanica in Pacific Panama were characterized by historical collapses and recoveries that finally ended in the 1940s; oyster populations have not recovered since then. This study provides a baseline and meta-analysis of current P. mazatlanica densities in Las Perlas and Coiba Archipelagos. We compared the oyster densities in relation to substrates and depths at 103 sampled sites using randomization techniques. Mean oyster density per site ranged from 2.8–238.9 ind·ha⁻¹ in Las Perlas and 6.0–263.9 ind·ha⁻¹ in Coiba. These values are one to three orders of magnitude lower than those reported for La Paz, Baja California (3,000–12,000 ind·ha⁻¹) and Costa Rica (24,200 ind·ha⁻¹) in recent times. Substrates within the archipelagos were diverse. We found an increasing trend of density variance when regressing log-transformed densities against substrates ordered according their increasing availability of hard surfaces. In Coiba, densities in substrates including rocks plus corals and sand were statistically lower in shallow than in deep waters, probably caused by harvest. The highest densities in Las Perlas occurred southeast of Del Rey and western Saboga islands. In Coiba, we found the highest densities in Ranchería Island and on the westernmost side of Coiba and Jicarón Islands. These data will help to define the environmental framework within which future research on this important species must be conducted and can be used to improve plans to address its management and conservation.