In this paper, two wavelengths mainly used for laser prostatectomy have been quantitatively compared: 532 and 980 nm. Two lasers at 40 W were employed to ablate bovine liver in vitro. Ablation performance was evaluated in light of number of sweeps, ablation volume, and coagulative necrosis. 532 nm yielded up to four times higher ablation efficiency than 980 nm. Regardless of wavelength, ablation rate per sweep decreased with the number of sweeps. 532 nm generated relatively deeper ablation craters along with thinner coagulation whereas 980 nm created superficial tissue ablation with up to 2 mm thick coagulative necrosis. Due to higher light absorption and effective thermal confinement, 532 nm induced more efficient tissue ablation with a smaller coagulative necrotic zone. The current study demonstrated that 532 nm could be a more ideal wavelength for laser prostatectomy, and the future in vivo investigations will confirm these findings.