The present study aimed to detect the most prevalent serogroups and circulating Leptospira species in cows from Brazilian Amazon. Samples of blood serum, urine and kidney of 208 animals were collected at a municipal slaughterhouse in the Baixo Tocantins region of Pará State, Northern Brazil. The tests used were microscopic agglutination test (MAT), bacteriological isolation, polymerase chain reaction (PCR) and DNA sequencing. The frequency of MAT-reactive cows was 46.6% (97/208) with titers ranging from 100 to 3200, being Sejroe serogroup the most prevalent. There was no Leptospira isolation, but the DNA of bacterium was detected in 5.8% (12/208) of the kidney and in 14.9% (31/208) of the urine samples. DNA sequencing was performed directly from PCR products of 30 samples (3 kidneys and 27 urines), with identification of four different species: L. borgpetersenii with 56.7% (17/30), followed by L. kirschneri with 13.3% (4/30), L. interrogans with 6.7% (2/30), L. santarosai with 3.3% (1/30), and 20.0% (6/30) of samples were identified only at the genus level. These results reveal a diversity and peculiarity for bovine leptospirosis in the Amazon region, mainly due to the low frequency of L. santarosai and more surprising, the presence of L. kirschneri, differently of what is observed in other regions of Brazil.