The binary toxin (Bin) from Bacillus sphaericus consists of two polypeptides, BinA (42 kDa) and BinB (51 kDa) that work together to kill susceptible mosquito larvae. To investigate the functional regions of BinA involved in the interaction with BinB, four BinA truncated fragments, from both N- and C-termini, were constructed and expressed in Escherichia coli. Neither individual nor a mixture of fragments of BinA showed larvicidal activity against Culex quinquefasciatus larvae even using a high dose of toxins. Far-Western dot blot analysis showed strong binding of both C-terminal fragments (17 and 28 kDa) to BinB protein. This is the first report to demonstrate that the C-terminal part of BinA plays an important role for the interaction with BinB.