Objectives: To investigate the differences of genotypic distributions among isolates between immunosuppressed and immunocompetent patients in a Taiwanese population. Methods: Human cytomegalovirus (HCMV) isolates from 76 patients with adequate chart data were analyzed. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to define gB genotypes which include gB1 to gB4. The clinical data of the 76 patients were retrospectively collected by chart review and classified into an immunosuppressed (n = 32) or immunocompetent (n = 44) group. Results: Among the 32 immunosuppressed patients, the most commonly identified HCMV genotypes were gB1 (27/32, 84.3%) and gB3 (4/32, 12.5%). 59.1% (26/44) of the immunocompetent patients were infected by gB1 while 38.6% (17/44) of them were infected by gB3. The frequency of gB1 infection in the immunosuppressed group was significantly higher than that in the immunocompetent group (p = 0.025). However, there was no statistically significant difference between gB1 and gB3 distributions by clinical diagnosis within each group. Conclusions: Only gB1 and gB3 genotypes were identified in this Taiwanese population. Although there is no significant difference between clinical diagnosis and gB genotyping, gB1 infection is significantly more predominant in immunosuppressed patients.