| Summary: | The estimated prevalence rate of adults living with HIV infection in MENA is one of the lowest in the world. To date, no data on the genetic characteristics of <i>Cryptosporidium</i> isolates from HIV/AIDS patients in Algeria were available. This study aimed to identify <i>Cryptosporidium</i> species and subtype families prevalent in Algerian HIV-infected patients and contribute to the molecular epidemiology mapping of <i>Cryptosporidium</i> in the MENA region. A total of 350 faecal specimens from HIV/AIDS patients were analysed using microscopy, and a <i>Cryptosporidium</i> infection was identified from 33 samples, with 22 isolates successfully sequencing and confirming species and subtypes. Based on sequence analysis, 15 isolates were identified as <i>C. parvum</i> with family subtypes IIa (<i>n</i> = 7) and IId (<i>n</i> = 8), while five were identified as <i>C. hominis</i> (family subtypes Ia (<i>n</i> = 2) and Ib (<i>n</i> = 3)) and two as <i>C. felis</i>. The <i>C. parvum</i> subtype families IIa and IId predominated, suggesting potential zoonotic transmission. More extensive sampling of both humans and farm animals, especially sheep, goats and calves, as well as a collection of epidemiological data are needed for a better understanding of the sources of human <i>C. parvum</i> infections in Algeria.
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