Drought is a major constraint to the productivity of rice in the worldwide. The rice root system plays an important role in the regulation of water uptake and extraction from the deep soil layers. The objectives of this investigation were to study the variation in root morphology, some physiological traits, yield and its components and genetic diversity among some Egyptian rice varieties and some upland rice accessions under normal and drought conditions. Four upland rice accessions originated from Cote de Ivoire (IRAT112, IRAT170, WAB450-I-B-P-105-HB and Yun Len62) compared with three Egyptian rice varieties (Giza177, Sakha101 and GZ7456-13-6-5-3) were used in this investigation. Significant variation was observed in most of the investigated root traits such as root length, root volume, root thickness and root dry weight among the upland rice accessions and Egyptian rice varieties. Also there are a significant variation in some physiological traits which were related to fitness and productivity, including yield and its components under normal and drought conditions. This indicated that the upland rice accessions are tolerant to drought via its have good root system compared with the Egyptian rice varieties which were sensitive to drought.　Most of the traits showed significant and highly significant correlation. Genetic diversity among the Egyptian rice varieties and upland rice accessions was studied with microsatellite markers. One hundred and forty alleles were detected with 80 SSR markers among all the rice accessions. 　The highest genetic relationship as revealed by SSR markers was detected among Giza 177, Sakha 101 and GZ7456-13-6-5-3 as japonica type, on the other hand there were some similarity between Egyptian rice varieties and each of WAB450-I-B-P-105-HB and Yun Len62. While, the lowest similarity was found among the Egyptian rice varieties and upland rice accessions IRAT 112 and IRAT 170 as indica type. Two dendrograms have been created based on 80 DNA markers (SSR primers) and 17physiologcal traits data for seven accessions and compared. Cluster analysis grouped the rice genotypes into three classes in which japonica type, Giza177, Sakha101 and GZ7456-13-6-5-3 in group1, meanwhile, WAB450-I-B-P-105-HB and Ynlen62 clustered in group 2. On the other hand IRAT112 and IRAT170 were clustered together as indica type in group 3. Based on this investigation the larger range of similarity values among varieties using microsatellites provides greater confidence for the assessment of genetic diversity and relationships.