Follicular apoptosis in the tropical mussel Mytella strigata was assessed in three coastal lagoons located in the southern Gulf of California, Mexico. Mussels were collected from three coastal lagoons associated with different scenarios of anthropogenic stress during one year. The gonad of each mussel was dissected, weighed, and sampled for histology and apoptosis analysis by TUNEL labeling. Two apoptotic indices were used: the apoptotic index of cells (AIC) based on the number of follicular cells in apoptosis in one thousand cells counted per gonad, and the apoptotic index of follicles (AIF) based on the number of follicular cells per follicle per gonad. Both indices showed high association with each other for all developmental stages, although AIF seemed to better discriminate among sites. Higher AIF and AIC were observed at the Urias Estuary (1.6 and 1.5 respectively) ranked as highly polluted, followed by Ensenada del Pabellon (0.82 and 0.95 respectively), ranked as moderately polluted, and the Teacapan Estuary (0.57 and 0.76 respectively) ranked as slightly polluted. Our data indicate that the apoptotic index in tropical mussels could be a useful indicator of environmental stress in coastal ecosystems; however, the ecological relevance of follicular apoptosis in polluted environments needs further investigation.