Trypanosoma evansi is the parasite responsible for causing Surra, a significant veterinary disease worldwide. The development of drug resistance is a major obstacle in controlling trypanosomosis. Typically, drug resistance occurs due to changes in the drug transporters of parasites. However, the prevalence of drug-resistant trypanosomes in Egypt's endemic regions is not well understood. In this study, we analyzed the TbAT1 and AQP2 genes from six T. evansi strains collected from camels a cross various locations in Egypt. PCR was utilized to amplify 164 bp TBR1/2 primers, followed by the amplification of 1600 bp and 1416 bp regions corresponding to the adenosine transporter P2 gene and the aquaglyceroporin transporter gene, respectively. Sequencing and BLAST analysis were conducted to compare the sequences with those in GenBank, and phylogenetic analysis was performed on all strains related to the TBR1/2, AQP2, and AT1 genes. All six DNA samples tested positive for the TBR1/2 primers. Three strains from South Sinai, Matrouh, and Halaib did not have both the AQP2 and TbAT1 genes, while the other three strains were positive for both genes. The AQP2 gene showed no variations at the nucleotide or amino acid level in any of the strains. However, the AT1 gene sequences had substitutions at different sites, which could contribute to drug resistance. The Behera strain did not show any variations at the nucleotide or amino acid level. Our findings revealed the presence of the TbAT1 gene in three out of six T. evansi strains, with some mutations. Additionally, three local strains lacked both the AQP2 and TbAT1 genes, potentially linked to drug resistance in T. evansi. This study provides molecular evidence of drug resistance in T. evansi in Egypt, which could be valuable for the treatment and control of Surra in the country.