Objective and Background: SEN virus has identified as a putative new hepatitis virus coinfected with hepatitis C in thalassemic patients. The study aimed to measure viremia with SEN virus among thalassemic patients infected and non-infected with hepatitis C virus (HCV). Further, to detect the genotype D and the genetic alterations in the internal transcribed spacer domains/regions of SENV-D genotypes. Patients and Methods: A total of 200 β-thalassemic patients were included. HCV-RNA and SEN-DNA are extracting automatically. Then, amplification for SEN-DNA by conventional polymerase chain reaction (PCR) was achieved. Furthermore, HCV-RNA was amplified using real-time PCR (RT-PCR). Sequencing analysis was also done for 14 samples of amplified SENV-D DNA. Results: Out of 100 positive ELISA-anti-HCV antibodies which were definite for RT-PCR, the mean viral load in these patients was 545806 ± 1,009,799 IU/ml (1,997,176 ±3,802,206) copies/ml. There was a significant increase in SENV-D in thalassemia patients without HCV infection (59%) than those in thalassemia patients with HCV infection (44%) and healthy subjects (7%). In a sequencing study, 11 samples were infected with D genotype only while three from thalassemia patients group were coinfected with D and H genotypes. Conclusions: The occurrence rate of SEN-V DNA in thalassemia patients is very high in Iraq. Further, SEN-V-D genotype is more prevalent, and the sequences of SEN-V-D nucleotides in persons with coinfection are the same sequences of persons that have an infection with SEN-V-D alone. The most countries which have similar sequences to Iraqi SENV-D genotype sequence are Iran followed by China, Japan, Brazil, and the United States of America.