Bothriurus bonariensis (Bothriuridae) is a scorpion species with a broad distribution in the Pampas biome in South America, causing low severity sting accidents each year. Possibly due to minor clinical interest, B. bonariensis venom has not been fully characterized concerning its molecular composition and may constitute an underestimated source of compounds with e. g. antimicrobial and insecticidal activities, valuable in drug discovery research. In a previous investigation on the venom from specimens captured in Southern Brazil, transcriptomics and proteomics approaches (collectively called "venomics") were used and the functional annotation of obtained sequences revealed the presence of many ion channel modulators, proteases, protease inhibitors, and antimicrobial peptides, indicating the potential of this venom as a source of molecules with biotechnological relevance. In this work, the exploration through B. bonariensis toxins is expanded, providing an in-depth computational analysis of structural features of the most abundant venom peptides. Several toxins were investigated using homology modeling as well as AI-assisted protein predictions, revealing some structural motifs that can be used to infer their activities. Also, some sequences that could not be annotated on the basis of homology were modelled, in further efforts to classify these unknown proteins. These results provided valuable information concerning the diversity of molecules present in B. bonariensis venom, encouraging further exploration of venoms from neglected taxa in the prospecting of novel compounds.