The angular angelshark (Squatina guggenheim) is a coastal endangered angel shark and one of the major bycatch victims. Despite major concerns about this species, little is known about its evolutionary connectivity among its whole geographic distribution. Here, genetic connectivity and phylogeographic patterns of S. guggenheim for 122 individuals were assessed across Southwest Atlantic Ocean regions based on a multilocus mitochondrial DNA approach in order to support conservation strategies. The concatenated mitochondrial dataset (control region [CR], cytochrome b [CytB] and cytochrome c oxidase I [COI]) showed high levels of haplotype diversity and low nucleotide diversity in S. guggenheim, with distinct genetic diversity patterns among populations. Although signs of stepping-stone gene flow were observed, a strong and statistically significant genetic structure into at least four populations was detected, matching with the species' biological traits and region's oceanographic particularities. The phylogenetic analysis revealed the presence of two matrilineal lineages that diverged during the Pliocene. Contrasting demographic patterns were detected, in which only south-southwest Atlantic populations showed signs of population expansion. Despite the existence of connectivity among regions, our results suggest that conservation plans should be carried out following the uniqueness of each management unit.