The main purpose of this study was to clarify the role of gray marmots (
Marmota baibacina
) in the long-term maintenance of highly virulent strains of
Yersinia pestis
in two plague endemic foci of the Tien Shan Mountains in Kyrgyzstan. We present data from regular observations of populations of
M. baibacina
and small rodents cohabiting with marmots in the mountainous grasslands of the Sari-Dzhas (east of Issyk-Kul Lake) and the Upper-Naryn (south of Issyk-Kul Lake) natural foci. During 2012–2017, an abundance of marmots and their ectoparasites (fleas and ticks) was significantly higher in Upper-Naryn comparing to Sari-Dzhas, although there were no differences in a number and diversity of small rodents cohabiting with marmots. The plague bacterium was detected either in marmots or in their ectoparasites collected during 4 of 6 years of observation in Sari-Dzhas and during 2 of 4 years of observation in Upper-Naryn. Plague was found in three sectors situated closely to each other in Sari-Dzhas and in 1 of 8 repeatedly surveyed sectors in Upper-Naryn. During 6 years, we isolated 9 strains of
Y. pestis
from marmots, two from their fleas
Oropsylla silantiewi
, one from an unidentified tick, and one from the gray hamster (
Cricetulus migratorius
). All plague strains isolated from the rodents and their ectoparasites in this study were similar to
Antiqua
biovar specific for marmots. The results indicate that plague can circulate continuously in the Tien Shan Mountains in populations of gray marmots and their ectoparasites with a facultative involvement of other rodent species after significant changes in rodent communities that happened in Kyrgyzstan during the previous two decades. The simultaneous field survey of two natural foci of plague, Sari-Dzhas, and Upper-Naryn, would be important for further analysis of circulation of
Y. pestis
strains belonging to
Antiqua
biovar in the Tien Shan Mountains.