It's not always possible to obtain samples from dead male pinnipeds that are fresh enough to determine the histological characteristics of spermatogenesis and their stage of sexual maturity. We propose that the morphometrics of genital organs of northern fur seals, Callorhinus ursinus, can be used as a new indicator of sexual maturity. We analyzed data from collected records of male fur seals around Hokkaido during 2011–2017 to examine morphometrics of genital organs and their stage in histological characteristics of spermatogenesis. First, we investigated ontogenetic and seasonal variation in three genital organs: testes, epididymides, and bacula. Second, we classified the stages of histological characteristics of spermatogenesis into three groups (Stage A–C) using non-linear discriminant analysis, based on the stage in histological characteristics of spermatogenesis determined by histological observation of seminiferous tubules. Testicular size, testicular mass, and epididymal mass showed seasonal variation associated with spermatogenesis. From our analysis, the stage in histological characteristics of spermatogenesis could be estimated using testicular mass with high accuracy of predicting spermatogenesis. And measurement of baculum was suggested to be an indicator of predicting sexual maturity. We conclude that this simple estimation may be used to determine sexual maturity based on individual growth patterns.