Mercury (Hg) was measured in the muscle, liver, and gonads of Haemulopsis elongatus and Pomadasys macracanthus from Mazatlán (SE Gulf of California) to determine the relationships of the hepatosomatic index (HSI) and gonadosomatic index (GSI) of fish with Hg concentrations in the corresponding tissues. Health risk to consumers was assessed by using the hazard quotient (HQ), considering the average rate of fish consumption in Mexico and Hg concentration in the edible tissue. In H. elongatus, the highest Hg levels were measured in the liver (3.748 μg g−1); in P. macracanthus, the highest Hg concentration was quantified in the muscle (0.574 μg g−1). In P. macracanthus, the HSI was negatively correlated with Hg concentration in the liver; in H. elongatus, there was also a negative relationship between Hg levels in gonads and the GSI. Mean HQ values in Haemulopsis elongatus (0.005) and Pomadasys macracanthus (0.002) were below the value (HQ ≥ 1) of concern. The significant reduction of HSI and GSI with Hg increase in the liver and gonads may suggest that Hg bioaccumulation in these fish shows adverse physiological effects. Though HQ values in both species were below the unit, i.e., the consumption of the muscle from this species does not represent a health risk, it is necessary to carry out surveys of fish consumption rates in coastal areas of Mexico to do a more precise health risk assessment associated to Hg intake.