Abstract Maize is a valuable source of starch, but many genotypes still have not yet been studied. Thus, an ongoing research topic is to evaluate the physicochemical, structural, and functional properties of these understudied genotypes, such as is the case of the cacahuacintle maize genotype. Two cacahuacintle maize varieties MA1 and MA2, endogenous to the State of Mexico but from different locations, are used for obtaining maize starch (MS1 and MS2) and compared to a commercial normal maize starch (CS). Scanning electron microscopy (SEM) reveals that CS granules have polyhedral shape, while those for MS1 and MS2 are semi‐spherical. Fourier‐transform infrared (FTIR) spectra shows that the three starches exhibit the characteristic peaks of polysaccharides but display differences in the hydrated and ordered structures. X‐ray analysis reveals that all the starches have Type A pattern, but have different crystallinities, ranging from 21.07% to 25.37%. MS1 and MS2 exhibit higher values of solubility, swelling power, and water retention capacity compared to CS, but the latter has superior oil‐holding capacity. MS1 and MS2 have higher resistant starch fraction content than CS. The results show that cacahuacintle maize starch has a good application potential as an additive in food products.