Genetic diversity in agro-morphological traits and molecular markers was assessed among sorghum landraces (Sorghum bicolor L.) collected from three agro-climatic regions in Upper Egypt. Days to 50% flowering, plant height (cm), panicle length (cm), panicle width (cm), thousand grain weight (g), number of grains panicle-1 and grain yield panicle-1 (g) were evaluated in two successive seasons. Molecular diversity was also assessed by RAPD and ISSR markers. The results indicated significant differences among genotypes for the agro-morphological traits and clustering based on these traits classified the genotypes into two single branches and three main clusters. A total of 109 DNA fragments were amplified by 10 primers from all landraces with an average 10.9 bands/primers. A total of 64 fragments (58.72%) showed polymorphism. Based on combined RAPD and ISSR data, the highest genetic similarity (0.963) was observed between Assuit 31-94 and Assuit 32-94 landraces and the lowest relatedness (0.81) was observed between Assuit 132-94 and Assuit 52-93. Cluster analysis based on a combined RAPD and SSR data set revealed four major distinct groups. Positive correlation was found between two molecular markers (r = 0.267, p = 0.001). A low correlation (r = 0.083, p = 0.001) was found between the morphological dissimilarity matrix and the matrices of genetic dissimilarity based on RAPD and ISSR markers. From the result of this study, it was found that combination of morphological and molecular markers may be useful in studying genetic diversity of sorghum for conservation, breeding and other crop improvement activities.