Forty‐six converted exotic sorghum lines representing all five races and nine intermediate races of sorghum were fingerprinted using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. A total of 453 scored AFLP and SSR loci were used to calculate genetic similarities between the lines. The dendrogram constructed using UPGMA grouped 31 lines into three major clusters with Jaccard coefficients greater than 0.75. The remaining 15 lines were grouped into four small sub‐clusters each with two lines and seven single accession nodes. Phenetic analysis using AFLP and SSR markers resulted in clusters corresponding to the kafir, guinea, caudatum and durra morphological groupings. Cluster and principal coordinate analyses indicate that the guinea, kafir and intermediate lines in this study are more closely related than phenotype would suggest. Likewise, caudatum and intermediates involving caudatum showed close genetic relationship with durra and durra intermediates. For the most part, morphological classification of race based on panicle traits was also reflected by similarity in DNA based polymorphisms. The molecular diversity of bicolor and associated intermediate races is not reflective of their common morphological classification, since this race and its intermediates are quite heterogenous.