In Brazil, the use and diversity of the common names of fish species, coupled with taxonomic uncertainties, hinder the reliability of fishing statistical data. In this scenario, there are the so-called pilombetas of the São Francisco River, an important fishing resource in region. Despite its importance, the real diversity of species identified in the area remains obscure. In order to properly identify and delimit the species popularly known as pilombetas, an integrative approach involving traditional taxonomy, geometric morphometrics and molecular systematics was applied. Results from geometric morphometrics and molecular analyses were consistent with the results of the traditional morphological analysis, also indicating the delimitation of six taxa belonging to Engraulidae in the lower São Francisco River. In addition, species delimitation methods revealed an intrapopulation genetic divergence of 1.7% for Lycengraulis grossidens. The results revealed that the currently known richness species of Engraulidae in the studied area has been underestimated. Thus, an updated taxonomic key is herein proposed for the Engraulidae species from the lower São Francisco River and estuary. The integrative analysis approach revealed to be effective to address taxonomic questions and help the management of stocks, ensuring the maintenance of local diversity of fishes in the Neotropical region.(AU)