The Cry48Aa/Cry49Aa binary toxin from Lysinibacillus sphaericus is composed of a three-domain Cry-like toxin (Cry48Aa) and a binary-like protein (Cry49Aa) that work together to kill Culex quinquefasciatus mosquito larvae through a novel interaction between its two components. The aim of this study was to identify the functional regions of Cry48Aa that were involved in the interaction with Cry49Aa. Eight Cry48Aa truncated fragments were constructed from both N- and C-termini and expressed in Escherichia coli. Only the individual or combined N69K truncated fragment, a Cry48Aa N-terminal derivative consisting of three domains, showed larvicidal activity against C. quinquefasciatus larvae, while the other fragments exhibited significant loss of biological activity. Far-Western dot blot analysis showed that Cry48Aa N-terminal regions had the ability to bind to Cry49Aa protein. These results demonstrate that the N-terminal domain of Cry48Aa plays a crucial role in responsible for the full virulence to mosquito larvae and the interaction with Cry49Aa as a binary toxin.