Microgeographic variation in shell growth rate of Mercenaria mercenaria (L.) among habitats within the Indian River, Florida, was studied to develop a baseline against which the significance of M. mercenaria shell growth rate differences observed over a larger geographic scale could be compared. Hard clams of the genus Mercenaria were collected from 525 randomly located stations within the Indian River during July and August, 1986. Clams (n = 922) were returned to the laboratory and taxonomically identified using diagnostic protein loci. Clams identified as M. mercenaria (n = 465) were isolated and their shell growth rate determined by internal shell growth-increment analysis. The annual pattern of internal shell growth-increment formation in genetically identified M. mercenaria from the Indian River was documented using specimens collected monthly from September 1987 through August 1988. The translucent (slow growth) increment was deposited during summer and fall, whereas the remainder of the year was characterized by formation of the opaque (rapid growth) increment. This pattern is similar to that described for other hard clam populations from the southeastern United States. To compare shell growth rates of M. mercenaria among habitats within the Indian River, we used the omega-parameter of Gallucci and Quinn. The range of variation in omega-among habitats within the Indian River was similar to that observed for hard clams in Narragansett Bay, Rhode Island, but less than that observed for hard clams from various sites throughout the state of Florida. Shell growth rates of M. mercenaria in the Indian River increased with decreasing depth, and shell growth rates were more rapid in areas characterized by the presence of submerged aquatic vegetation than in areas devoid of such vegetation. Results of this study indicate that comparisons of shell growth rates among hard clam populations over a wide geographic range must be tempered by a consideration of shell growth rate variation among habitats within each site.