Histoplasma capsulatum is the etiological agent of histoplasmosis, which can infect birds and different mammal species, including humans. In Brazil, the disease is not notifiable, and little is known about its infection in domestic and wild mammals. This study aimed to perform the molecular detection of H. capsulatum in small wild mammals from peri-urban forest remnants and in dogs and cats peri-domiciled in rural communities adjacent to these fragments in the Pará State, Brazilian Amazon. Samples of lung, liver, and skin were collected from free-living rats and marsupials captured in three peri-urban forest patches, as well as blood and skin from dogs and cats. H. capsulatum DNA was detected by nested PCR amplification, with products sequenced and subjected to phylogenetic analysis. H. capsulatum DNA was detected in 9.5% (12/126) of small wild mammals, with rats having a higher frequency of positive animals (25.6%; 10/39) when compared to marsupials (2.3%; 2/87) (
p
=
0.0001
). The frequencies of positive dogs and cats were 1.6% (2/121) and 5.5% (1/18), respectively. A higher frequency of infection by H. capsulatum was observed among small wild mammals when compared to dogs and cats (
p
=
0.0143
). In conclusion, H. capsulatum infection occurs in rats, marsupials, dogs, and cats in the Brazilian Amazon, with rats being important sentinels of the presence of this fungus in areas of remaining forest.