The exogenous simian type D retroviruses (SRV/Ds) are prevalent in macaque monkeys and sometimes cause immunodeficiency with anemia, weight loss, and persistent unresponsive diarrhea. SRV/D isolates are classified as subtypes 1 to 6, and the entire sequences of the gag region of SRV/D-1, -2, and -3 and SRV/D-Tsukuba (SRV/D-T) have been determined. We designed specific primers in the gag region of SRV/D-T that enabled us to directly detect by polymerase chain reaction (PCR) SRV/D-T proviral DNA sequences in DNA extracted from whole blood. Using this assay and another PCR assay that detects multiple SRV/D subtypes, we performed a survey for SRV/D infection in our specific pathogen-free (SPF) and conventional colonies at Tsukuba Primate Center (TPC). In the SPF colony, no SRV/D signal was detected in any animal. On the other hand, SRV/D-T was detected in 11 of 49 animals (22.5%) in the conventional colony. SRV/D-T was the only SRV/D subtype detected. Consequently, SRV/D-T is the major SRV/D subtype present in cynomolgus monkeys at TPC.