Although bilateral animals, including Drosophila, appear to have left-right (LR) symmetry from the outside, their internal organs often show directional and stereotypical LR asymmetry. The mechanisms by which the LR axis is established in Drosophila have not been studied well. We showed that two type I Myosin proteins play crucial roles in the manifestation of Drosophila handedness. Mutants of Myosin31DF (Myo31DF), which encodes a type ID Myosin, showed reversed laterality of the embryonic and adult gut and testis. Myo31DF was required in the epithelial cells of the embryonic hindgut, where its protein co-localized with actin filaments, for the correct handedness of this organ. Disorganization of the actin cytoskeleton in the hindgut epithelium caused LR defects of the embryonic hindgut. These results suggest that the actin-based Myo31DF function is required for proper handedness. In contrast, the disruption of microtubules in the hindgut epithelium did not affect the laterality of this organ. We also found that the overexpression of Myosin61F (Myo61F), which encodes another type I Myosin in the hindgut epithelium reversed the hindgut handedness, suggesting that these two type I Myosins--Myo31DF and Myo61F--have antagonistic functions. We propose that the actin-based functions of type I Myosins play critical roles in generating LR asymmetry in invertebrates.