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Simple Summary: The expansion of human activities into natural areas increases contact between humans, domestic animals, and wildlife, which can facilitate the circulation of infectious agents between these species, leading to the emergence of zoonoses. Several studies have investigated the role of animals, including reptiles, as possible carriers of the Leptospira bacterium. This study aimed to detect the DNA of the bacterium in Kinosternon scorpioides turtles kept in captivity in a region of the Brazilian Amazon. Blood, cloacal fluid, cloacal lavage, and stomach lavage samples were collected from 40 turtles. Of these, 40% of the animals tested positive for Leptospira. Genetic analysis confirmed the identification of the bacteria, which could pose a risk to public health. Handling infected animals could increase the risk of transmitting the disease, especially considering that turtle meat is consumed in the region. This study is the first to detect Leptospira in the blood of chelonians, confirming exposure to the pathogen. Although the turtles showed no abnormal clinical signs, it is possible that the clinical signs are unknown in reptiles. In conclusion, captive K. scorpioides turtles have been exposed to Leptospira. Leptospirosis is a zoonosis of great importance for One Health. In this context, the Amazonian biome may harbor numerous hosts for Leptospira spp. that contribute to the maintenance of the pathogen in the environment. Some reptiles, such as chelonians, have been little studied in terms of their involvement with leptospires. The objective of this study was to detect Leptospira spp. DNA in Kinosternon scorpioides turtles kept in captivity in a region of the Brazilian Amazon. A total of 147 samples of blood (n = 40), cloacal fluid (n = 27), cloacal lavage (n = 40), and stomach (n = 40) were collected from 40 chelonians. After DNA extraction, the samples were subjected to amplification of a 331 base pair product of the 16S rRNA gene using the Lep1 and Lep2 primers. PCR products were Sanger sequenced, assembled, and subjected to online blast search and phylogenetic analysis. Of the animals tested, 40% (16/40, 95% confidence interval [CI]: 25–55) had at least one or two samples positive for Leptospira spp. Considering the total number of samples collected, 12.93% (19/147) were positive, being blood clots (27.5%; 11/40), followed by cloacal washings (10%; 4/40), cloacal fluid (11.11%; 3/27) and gastric washings (2.5%; 1/40). Of these, 11 samples were sequenced and showed 99% to 100% identity with Leptospira interrogans sequences, which was confirmed by phylogenetic analysis. This is the first study to detect pathogenic Leptospira DNA in chelonians in a region of the Brazilian Amazon. It has been concluded that K. scorpioides turtles in captivity have been exposed to pathogenic Leptospira. [ABSTRACT FROM AUTHOR]