Selection for genetic modifiers of starch and sugar accumulation in sugary1‐ref (su1‐ref) maize (Zea mays L.) has led to the improvement of flavor characteristics in su1 sweet corn hybrids. The Su1 gene encodes a starch debranching enzyme that when defective causes large quantities of water‐soluble polysaccharides (WSP) to be produced in maize endosperm tissue. Another gene in maize, Isoamylase2 (Isa2), produces a starch debranching enzyme known to interact with the wild‐type SU1 protein in developing maize endosperm. Experiments were conducted to determine if a mutant of the Isa2 gene significantly modifies carbohydrate composition in su1‐ref inbreds and therefore is potentially useful for modifying flavor characteristics of su1 sweet corn. Using isa2–339, a mutant at the Isa2 locus, a population was created in which the su1‐ref and isa2–339 alleles were segregating. Lines developed from this population were used for single kernel carbohydrate analysis in 2012 and carbohydrate analysis of replicated ears in 2013. In 2012 and 2013, individual kernels and replicated ears fixed for the su1‐ref and isa2–339 alleles contained less starch and more total sugar compared with the su1‐ref, Isa2 parent, which was the source of the su1‐ref allele in this population. When the su1‐ref, isa2–339 mutant lines were reciprocally crossed with the Su1, isa2–339 parent, starch and WSP contents were significantly different among the Su1, isa2–339 parent and the hybrids. Kernels of both types of reciprocal hybrids had more WSP and less starch than did the Su1, isa2–339 parent. Kernels with two doses of the su1‐ref allele have more WSP and less starch than kernels with a single dose of the su1‐ref allele. In this population, starch content is further reduced in su1‐ref, isa2–339 double mutant genotypes compared with the su1‐ref parent. The su1‐ref/su1‐ref, isa2–339/isa2–339 lines developed in this experiment are the first documented double mutants of su1‐ref with another isoamylase starch debranching enzyme mutant.