This work evaluated the activity and ultrastructural and morphological alterations induced by the xanthone 1,3,7-trihydroxy-2-(3-methylbut-2-enyl)-xanthone (C23) isolated from Kielmeyera coriacea against Trypanosoma cruzi. This xanthone had inhibitory activity against the three forms of this protozoan and did not induce toxicity in mammalian cells. The best activity of this xanthone was against the intracellular amastigote form. Additionally, the mitochondrion was the main target of this compound, reflected by electronic microscopy and rhodamine 123 assays. Our MitoSOX assay results also indicated that C23 increased O2(-) production in mitochondrion. C23 might be a promising chemotherapeutic agent against T. cruzi because its trypanocidal action involves the disruption of mitochondrion, a specific target of Trypanosomatides.