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Isopisthus parvipinnis, commonly known as "bigtooth corvina", is a marine estuarine‐dependent fish captured in the southeast and south Brazilian coast as bycatch of the shrimp fishery. This work used the sagittae morphology as a tool to primarily study the population structure of I. parvipinnis between São Paulo and Santa Catarina states (23ºS to 26.9ºS) in Brazil. Secondly, it intended to verify the existence of morphological alterations over time, by comparing otoliths of fish captured in 1975 and 2018/2019. Otolith shape analyses were performed in individuals ranging from 66 to 139 mm of total length, obtained from historical (1975) and present catches (2018/2019) in the shallow coastal areas off North of São Paulo (NSP), Centre of São Paulo (CSP), South of São Paulo (SSP), Paraná (PR) and Santa Catarina (SC). Otoliths were analyzed using shape indices (SIs), elliptical Fourier descriptors (EFDs) and both tools combined. Morphological variations among locations and between years were tested using uni and multivariate statistics. Data showed regional differences in the otolith shape analysis over the years. Samples from 1975 presented an overall low reclassification rate (43%), with a high overlap of individuals among locations, suggesting the existence of a single group. Differently, samples from 2018/2019 discriminated four distinct spatial units with a good overall reclassification (74%): group 1 ‐ NSP; group 2 ‐ CSP; group 3 ‐ SSP + PR; and group 4 ‐ SC. The hereby data suggests regional changes at long term in the population dynamics of I. parvipinnis, from a single panmictic population in the past to a metapopulation structure in the present days, with consequences for the rational and sustainable management of the fishery. However, once it was the first evaluation of the population structure of I. parvipinnis, it is highly recommended to use complimentary phenotypic and/or genetic approaches to corroborate the hereby observed findings. [ABSTRACT FROM AUTHOR]