Camels are considered as integral and notable components of the heritage of the Kingdom of Saudi Arabia. Genetic variabilities within and among four camel populations in Saudi Arabia were evaluated using 21 simple sequence repeat (SSR) loci of 122 unrelated individuals, including three indigenous breeds [Humur (HA), Zurg (ZR), Shuguh (SG)] and one exotic breed [Sudanese (SN)]. Nineteen SSR markers generated multilocus fingerprints with a total of 225 alleles, a range of 4–23 alleles per locus, and an average of 9, 7, 7, and 6 alleles per locus in HA, ZR, SG, and SN populations, respectively. The mean multilocus F_ST value (0.034 ± 0.005) showed non-significant population differentiation. Mean observed heterozygosity values were 0.908 for HA, 0.860 for ZR, 0.919 for SG, and 0.887 for SN, which were higher than the expected heterozygosity. An excess of heterozygotes was observed, suggesting the presence of overdominant selection or the occurrence of outbreeding. Pairwise genetic distances indicated that the three indigenous camel breeds were genetically close to each other and genetically distant to the SN population. This genetic variability assessment by microsatellite analysis is important and useful for the conservation of local camel genetic resources as well as the future development of breeding programs.