The pectoral muscle index (IPM)(IPM = 100 MPM M−1, where MPM and M are the pectoral muscle and body masses, respectively) fin‐area and fin ray length were studied over a year in male and female three‐spined stickleback Gasterosteus aculeatus from a marine population (Öresund, Sweden) kept under simulated natural light and temperature conditions. A castration‐replacement experiment was used to test androgen effects on the IPM, fin‐area and fin ray length. Non‐breeding males were castrated or sham‐operated in winter (i.e. the fish had low levels of androgens). Castrated control and sham‐operated fish were implanted with empty Silastic capsules and castrated groups with capsules containing the androgens testosterone or 11‐ketoandrostenedione into the abdominal cavity. The experiment was terminated after 41 days, when the controls had matured. No morphological differences were found in pectoral fins between sexes during the year, except during the peak breeding season (May), where females showed larger fin‐area and longer fin ray in length compared to males. No effects of androgens treatment or of castration on pectoral fin‐area or fin ray length was observed. Breeding and non‐breeding males showed higher IPM compared to females. The lower IPM in females than in males could not be explained by the larger gonads in the former alone, as a sex difference in IPM was still present after deduction of the ovaries from the female body mass. The IPM was higher in sham‐operated compared to castrated fish. No effects of androgens treatment on IPM was observed.