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The lesser kestrel (Falco naumanni) is one of the most endangered bird species in Europe, and a captive breeding and reintroduction project was established. A breeding project is vulnerable to pathogens, e.g., mycoplasmas, reducing the reproductive success and carrying the risk to release pathogens with the birds to the wild. Therefore, 18 infertile eggs and 43 dead in shell embryos of the breeding project, as well as 27 nestlings and 34 adult birds of the captive and three different free-ranging populations were investigated for the occurrence of mycoplasmas by culture and a Mycoplasma genus-specific polymerase chain reaction. All eggs, embryos, and hand-reared nestlings from the captive group were negative. In contrast, all parent-reared nestlings and 88% of the adults were positive. Mycoplasma falconis and unidentifiable mycoplasmas were detected in all groups. Mycoplasma buteonis was found in the captive and only in two of the three free-ranging populations. Sequencing the 16S rRNA gene of six randomly selected unidentified isolates showed that five isolates were similar and most likely had been found previously in a falcon from Germany. The remaining isolate demonstrated a very high homology to unidentified Mycoplasma isolates obtained previously from semen samples of raptors. The results suggest that these isolates might represent two new species. Mycoplasmas seem not to play a major role as pathogens in the breeding project, and there is no evidence that releasing birds poses a risk to the free-ranging population with regard to mycoplasmas. The study seems to be the first to describe the occurrence and role of mycoplasmas in the lesser kestrel.