The Arabian camel (Camelus dromedarius), which is domesticated in semi-desert environments in Egypt, is one of the neglected animals in the scientific community. Although, it is the best model for studying acclimatization as it is well adapted to withstand severe drought and high temperatures and survive for long periods. Many physiological and behavioral aspects were found to play a role in such adaptations. At the molecular level, it is well known that heat shock genes play an important role in thermotolerance of camels. Therefore, this study was designed to investigate relationship among the most dominant breeds in Egypt (Fellahi, Maghrebi and Sudani) in order to determine the phylogenetic relationship based on sequences of two heat stress genes (HSP family B (small) member 9: HSPB9 and HSP 70 kDa 1B: HSPA1B). Both genes were isolated and partially sequenced from Fellahi, Maghrebi and Sudani Egyptian breeds. It has been deposited in the NCBI database with accession numbers MZ243318, MZ243319, MZ243320, MZ851990 and MZ851991. By studying the phylogenetic tree based on HSPB9 gene sequence, our results showed that Maghrebi and Sudani breeds are closely related whereas, Fellahi breed was found to be more related to the reference breed on database. Relying on HSPA1B gene sequence, it was found that Maghrebi breed is closely related to wild strain (Camelus ferus). Additionally, Fellahi breed was separated into distinct group with reference breed, which indicates strength of its relationship to reference origin.