This study investigated the prevalence and genotype distribution of Pneumocystis jirovecii in HIV-positive patients with pneumonia in Jakarta, Indonesia. A total of 100 sputum samples were collected from two hospitals and analyzed using real-time PCR targeting the P. jirovecii MSG gene to detect the presence of the organism. Genotyping was performed through mtLSU ribosomal DNA sequencing and DHPS gene restriction fragment length polymorphism (RFLP) analysis. P. jirovecii DNA was detected in 20% of samples (20/100). DHPS analysis revealed that 58.3% (7/12) of patients with P. jirovecii pneumonia carried resistant genotypes, including 16.7% genotype 3 and 41.7% mixed genotypes. Sequencing of mtLSU identified seven variants, with variant 3 being the most common and showing a strong association with lower CD4+ T-lymphocyte counts. These results suggest that multiple resistant genotypes of P. jirovecii are circulating in Indonesia and that resistance is more closely linked to the patient’s clinical condition and immune status than to mtLSU variant type. This study provides important molecular epidemiological data on P. jirovecii in HIV-positive patients in Indonesia and highlights the need for ongoing monitoring of genotypes and resistance markers to guide treatment strategies and improve patient outcomes. © 2026, Bulgarian Society for Microbiology (Union of Scientists in Bulgaria). All rights reserved.