In southern Taiwan, mudstone badland accounts for over 1000 km2 of the upstream region of watersheds. Rainstorms often induce interrill and surface erosion on the mudstone slopes. Furthermore, the large quantity of soils detached by surface runoff result in severe sedimentation in reservoirs. Thus, soil erosion control of mudstone badlands represents one of the most pressing problems in reservoir watershed management. Cynodon dactylon (L.) Pers. (Bermuda grass) and Eremochloa ophiuroides (Munro) Hack. (Centipedegrass) are two native predominant C4 grass species appearing on mudstone badlands. They play a key role in erosion control and the revegetation of mudstone slopes. Nevertheless, their root functional traits and water erosion-reducing potential have not been investigated. In this study, the root traits were examined. Vertical pullout and tensile tests were conducted to measure root pullout resistance and root tensile strength. Hydraulic flume tests were also performed to evaluate their water erosion-reducing potentials. The results demonstrated that the root systems of C. dactylon and E. ophiuroides grasses all belonged to the fibrous M-type. C. dactylon had remarkably better root traits compared to those of E. ophiuroides. Furthermore, the root tensile resistance of C. dactylon was remarkably higher than that of E. ophiuroides. In addition, hydraulic flume tests showed that C. dactylon has remarkably smaller soil detachment rates than that of E. ophiuroides. Altogether, our data clearly show that C. dactylon has better root traits, root pullout resistance, root tensile resistance and water erosion-reducing potential than E. ophiuroides and is more suitable for erosion control of mudstone badland. Further studies on large-scale implementation techniques of these species for efficient vegetation restoration are needed.