Populations of cave-dwelling bat species were investigated in the transitory region between the Eastern Thrace and the Western Pontus. Data were collected during 30 surveys in 13 underground sites, 10 of which had not been surveyed previously by bat researchers, between March 1999 and March 2000. Approximately 20000 bats representing eight species were recorded. Grouping the sites according to their ecological resemblance, by means of cluster and correspondence analyses, yielded different results for the summer and winter data. In summer, there was a partial separation of the sites by their location in biogeographic regions. In winter, no regional grouping was observed. It was concluded that in the transitory region, species distribution does not differ considerably between the Eastern Thracian and Western Pontic ecosystems. In addition, a conservation scoring system is proposed for those sites investigated, their status is evaluated, and the most important local roosts are identified.