SUMMARYHistoplasma capsulatumwas sampled in lungs from 87 migratoryTadarida brasiliensisbats captured in Mexico (n=66) and Argentina (n=21). The fungus was screened by nested-PCR using a sensitive and specificHcp100gene fragment. This molecular marker was detected in 81·6% [95% confidence interval (CI) 73·4–89·7] of all bats, representing 71 amplified bat lung DNA samples. Data showed aT. brasiliensisinfection rate of 78·8% (95% CI 68·9–88·7) in bats captured in Mexico and of 90·4% (95% CI 75·2–100) in those captured in Argentina. Similarity with theH. capsulatumsequence of a reference strain (G-217B) was observed in 71Hcp100sequences, which supports the fungal findings. Based on the neighbour-joining and maximum parsimonyHcp100sequence analyses, a high level of similarity was found in most Mexican and all Argentinean bat lung samples. Despite the fact that 81·6% of the infections were molecularly evidenced, only threeH. capsulatumisolates were cultured from all samples tested, suggesting a low fungal burden in lung tissues that did not favour fungal isolation. This study also highlighted the importance of using different tools for the understanding of histoplasmosis epidemiology, since it supports the presence ofH. capsulatuminT. brasiliensismigratory bats from Mexico and Argentina, thus contributing new evidence to the knowledge of the environmental distribution of this fungus in the Americas.