The age and growth of horse clams Tresus keenae from Seto Inland Sea (SIS) and Ise Bay, western Japan, were investigated using a water-based marking pen on the edge of sectioned shells, after which unstained translucent zones at the chondrophore could be clearly observed. The translucent zone was formed once per year during autumn. The ages of all the samples were determined. The most frequent shell length (SL) in SIS and Ise Bay populations were 100–120 mm and 120–140 mm, respectively and mainly consisted of 3-y-old and 4-y-old clams, respectively. Clams in the SIS were found to be younger by about 1 y and 20 mm smaller on average than the Ise Bay population. The age–SL relationships of clams from each area were analyzed, using the original von Bertalanffy growth function (VBGF), a VBGF with a biological intercept, and the Gompertz growth function. The original VBGF showed the best fit with the SIS dataset, whereas the Gompertz growth model showed the best fit with Ise Bay clams. The parameters for each growth model were significantly different between SIS and Ise Bay, which may be due to clams younger than 2 y and smaller than 80 mm SL that were present only in the samples from SIS. Faster growth rate of the VBGF in Ise Bay than that in SIS would be affected by higher water temperature during the season of rapid growth.