Hull thickness is an important component of seed quality, which effects dehulling ability, feed or food nutritional aspects and cooking times. A breeding objective in Lupinus angustifolius crop improvement is to reduce hull thickness and a rapid screening method is needed to efficiently screen genotypes. Optical coherence tomography (OCT) imaging using infrared illumination at 980 nm was used to compare hull thickness of genotypes of four lupin species. OCT-derived hull layer thickness correlated highly with actual hull thickness determined by environmental scanning electron microscopy (r = 0.90) and allowed reliable distinction between mutant (thin-hulled) and parent genotypes of L. angustifolius. The imaging could clearly penetrate lupin seed to a depth of approximately 200 μm. The use of OCT to measure hull thickness has the advantage that it is rapid and non-destructive and should be very useful in selecting thin hull lines of lupins and other species on a single seed basis in germplasm or progeny from crosses.