Two different species of hemoplasmas, Mycoplasma coccoides and M. haemomuris, are known to infect small rodents such as mice and rats. However, there are no previous reports of hemoplasma infection in capybara (Hydrochaeris hydrochaeris). The aim of our study was to determine whether these hemoplasmas might infect capybaras from Southern Brazil. Blood samples from 31 animals: 10 captive and 21 free-ranging capybaras were collected and packed cell volume and total plasma protein were measured. DNA was extracted and PCR assays for M. coccoides and M. haemomuris were performed. Using the M. coccoides-PCR assay 64% of the capybaras were positive, 80% free-ranging and 30% from captive animals. The prevalence of infection between the groups was significantly different (p=0.001). Sequencing of the nearly entire 16S rRNA gene from the positive samples suggested a novel hemoplasma isolate with identity of 92% with M. coccoides and 86% with M. haemomuris. All capybara samples were negative for M. haemomuris infection. DNA of a housekeeping gene was successfully amplified from all samples. This is the first evidence of a hemoplasma infection in capybaras.