An understanding of the effects of fishing on marine ecosystems relies on information about the conserved state of these environments. Non-conventional approaches such as the use of historical data and local ecological knowledge can provide information and help adjust our references of changes in the environment. Also, the combination of different types of data can indicate a fisheries trend that would be undetectable when evaluated separately. Here we investigated changes in fisher's perceptions regarding overexploited and new target species in artisanal fisheries in a secular fishing village of the subtropical, southeastern Brazilian coast. We identified temporal changes in landings and in the mean trophic level (MTL) of high trophic level species (≥ 3.5 and >4) over 16 years. Fishers' knowledge revealed shifts in perception associated with years of fishing practice. More experienced fishers recognized a greater number of overexploited and new target species than fishers in the beginning of their careers. Landing data has revealed declining trends of 72% for five mesopredators species. Due to the overfishing of mesopredators, there was a shift in target species, towards fish that were previously discarded. Temporal changes in landings and in the MTL metric are concordant with previous reports on the overexploitation of species caught by local fishers. Our work reveals that multiple sources of information can be combined to establish historical baselines and improve the detection of change in marine ecosystems.