Background: Cryptosporidium is an etiologic agent of gastro-intestinal disorders and severe, profuse watery diarrhoea in immunocompromised patients, such as people living with HIV/AIDS. Aim: This study was carried out to determine the genotypic and phylogenetic characteristics of Cryptosporidium parvum among HIV patients who usually received antiretroviral therapy (ART) in four selected hospitals in Maiduguri Metropolis. Study Design: This is a clinical laboratory study of opportunistic pathogens in HIV/AIDS Patients. Place and Duration of Study: This was conducted at the Department of Medical Laboratory Science, the University of Maiduguri in collaboration with the Biological Sciences Department, ATBU Bauchi, Nigeria, between March 2021, and February 2022. Methods: A total of 400 faecal specimens were collected from confirmed HIV-positive patients and screened for Cryptosporidium-specific antigen by Enzyme Link Immunosorbent Assay (ELISA). Genomic DNA Extraction was done by Quick-DNATM Faecal Microbe Miniprep with PCR amplification and sequencing of 18s SSU rRNA gene using specific reference primers. Results: Out of the 70 HIV/AIDS and Cryptosporidium co-infected patients, 20 of the samples contained 18s SSU rRNA genes, with the highest frequency (45.0%) found in patients from the University Teaching Hospital. The results of phylogenetic analyses indicated that there is significant intra-species diversity in the genus Cryptosporidium. The four human C. parvum isolates differ from the bovine and the two avian isolates in three regions of the 18s rRNA gene. Conclusion: The human genotype (genotype I) found in this study is exclusively human and in a single non-human primate, in bovine genotype (genotype II) has proved to be anthroponotic and zoonotic to the livestock. The study, therefore, advocates further genotyping of Cryptosporidium from both HIV-infected patients and immunocompetent hosts from various regions together with surveillance of animal and environmental reservoirs is highly recommended.