Abstract: The aim was to uncover the molecular mechanism of sweet and waxy in maize, hopping it to be useful in special-used maize breeding and developing some intragenic selection markers. Sweet maize and waxy maize are popular vegetable food and important materials for processing production. Their sweet and waxy characters are controlled, respectively by recessive genes sh2, bt1, bt2 and wx located at different chromosome loci. On molecular level, these recessive genes are mutated from the encoding genes of the key enzymes of starch biosynthesis pathway by the insertion of different transposon elements. The effort to breed double recessive sweet-waxy maize controlled by recessive sweet genes and recessive waxy gene is impractical, because sweet and waxy phenotypes can not be expressed in the same inbred line or hybrid for their exclusion in biochemical metabolism. The backcrossing procedure of the conventional breeding method for sweet maize and waxy maize can be cut down almost to half, if intragenic selection marker is developed on the basis of sequence difference between the dominant genes and the recessive mutated genes and used to identify the recessive genes from the segregating generations.