<p>The Threespine Stickleback (<i>Gasterosteus aculeatus</i>) exhibits remarkable morphological diversity among populations. Nevertheless, the majority of previous studies have investigated morphological variation at the adult stage, and less is known about the variation in ontogenetic morphological changes. In the present study, we investigated the developmental changes in body depth and head length in divergent populations of the Japanese Threespine Stickleback as well as the closely related species, the Japan Sea Stickleback (<i>Gasterosteus nipponicus</i>). Our research revealed a trend that sticklebacks that utilize estuarine or marine habitats exhibit ontogenetic changes in the growth rate of body depth and head length relative to standard length, with their growth rates increasing at a later developmental stage. In contrast, freshwater-resident populations showed little ontogenetic change in allometry. These results demonstrate that closely related species and even populations within a species can exhibit divergent developmental patterns with respect to morphological allometry.</p>