The elimination of Starch Synthase IIa (SSIIa) in durum wheat seeds increases amylose and protein but decreases starch and seed size. To mitigate the negative impact of increased amylose upon seed size we identified partially functional SSIIa alleles and combined them with SSIIa null alleles. The first step was to mutagenize durum with ethyl methanesulfonate (EMS) and select SSIIa-A1 and SSIIa-B1 missense alleles and combine them by crossing with SSIIa null alleles. Segregating lines possessing a SSIIa null mutation in one genome and a missense mutation in the other genome were compared to single SSIIa null mutant sister lines over two field seasons. Lines that carried one SSIIa null and one missense allele showed elevated amylose compared to single null sister lines and controls. In most SSIIa haplotypes tested, increased amylose content was negatively correlated with seed size and starch content. However, two SSIIa missense alleles were identified that increased amylose to 34 % when combined with a SSIIa null allele. Thus, moderate amylose increases are possible if a small amount of SSIIa activity remains in developing wheat seeds without negatively impacting seed size or starch.