Starch is an important polymer made up of amylose and amylopectin. ADP-glucose pyrophosphorylase (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDE) are involved in starch synthesis. SSI, SSIIa and SBEIIb associate in phosphorylation-dependent multi-subunit complexes in maize. This investigation aimed to characterize new mutations in the SBEIIb gene using a TILLING technique. A single nucleotide substitution (G>A) in the SBEIIb gene was generated, translating to a cysteine to tyrosine amino acid change (C663Y) in a putative protein-protein interaction domain. C663Y SBEIIb appears to have reduced activity compared to the reference genotype, and the SBEIIb-SSIIa interaction is weakened. Starch granules from the C663Y mutant appear to possess SBEIIb as well as another branching isoform, SBEI, which is not normally found in the starch granule. The work presented here suggests altered protein-protein interactions in the C663Y mutant resulting in a change in starch structure.