Relationships among shell shape, shell growth rate, shell thickness, and nutritional condition in the Manila clam (Ruditapes philippinarum) collected from various areas in Japan were analyzed to establish an easy and quick way of determining stock condition in a harvest area. There were significant local differences in “shell sharpness indices” (i.e., shell height and width relative to shell length) and relative shell thickness (i.e., shell thickness relative to daily shell length growth), which became insignificant after eliminating effects of nutritional level as determined by a condition factor for each individual, indicating that nutritional condition modifies shell shape, and therefore shell shape may be used as an index of nutritional condition regardless of locality. Individuals with a better nutritional condition had smaller relative shell thickness, and tended to have more elongate and flatter shells. Shell width relative to shell length was considered to be a better index of nutritional condition than shell height relative to shell length. Shell morphology also reflected moisture content of the flesh, which is an important measure of palatability. Shell length growth rate did not have a significant correlation with absolute values of shell thickness; however, it had a negative correlation with relative shell thicknesses and sharpness indices, indicating that faster growing individuals have relatively thinner and flatter shells. Thus, shell shape and thickness have been shown to be an indicator of growth rate and nutritional condition in R. philippinarum. Clam fishers and farmers may use this method to determine stock condition for making decisions, such as harvest timing, culling of excess clams, and translocation of clams to better locations for enhanced production.