Trypanosoma cruzi, the etiological agent of Chagas disease, is a parasite with variable tissue tropism according to its genotypic variants. During chronic human infection, cardiac tissue is the most commonly affected, less frequently the digestive tract. Although not confirmed, the TcI genotype is associated with cardiac infection while TcII with the digestive tract. Traditional in vivo models for T. cruzi are opaque; thus, it is not possible to visualize live parasite behaviour, hindering studies of parasite-host interaction. The goal of this study is to evaluate cardiac tropism of TcI and TcII trypomastigotes in zebrafish larvae. Labelled trypomastigotes were injected into the duct of Cuvier of zebrafish larvae and tracked by stereomicroscopy and light-sheet fluorescence microscopy. TcI parasites adhered to the atrium, atrioventricular valve, and circulatory system were identified. TcII trypomastigotes adhered to the atrium, atrioventricular valve and yolk sac extension were also observed. When simultaneously injected, both TcI and TcII attached to the heart; however, TcII trypomastigotes attached in higher numbers. Although the TcII variant has previously been associated with digestive tract infection, both variants have cardiac tissue tropism in this in vivo model, and studies to establish the extent of cardiac infections by TcII should be made.