The zeins, slat-soluble proteins and random amplified polymorphic DNA (RAPD) markers were used to detect the genetic diversity among 16 maize inbred lines and to conduct the heterotic grouping for these 16 inbred lines. Thirteen random primers were identified with polymorphism and reproducibility among the tested materials. The numbers of polymorphic bands of zeins, salt-soluble proteins and RAPD markers were 30, 34 and 112, respectively, which were about 83.3, 85.0 and 86.8% of total alleles, respectively. A comparison of genetic similarity matrices revealed that correlation coefficients based on zeins, salt-soluble proteins and RAPD markers were significantly correlated. The average genetic similarity coefficients of three markers (zeins, slat-soluble proteins and RAPD) were 0.597, 0.541 and 0.554 and were consistent with each other, but the standard deviation of the genetic similarity coefficient based on RAPD was the smallest. These inbred lines were classified into three, three and four groups, respectively, based on zeins, salt-soluble proteins and RAPD markers data, which were all consistent with the grouping based on the available pedigree data, except for some discordance.