Extended wavelength InGaAs photodiodes in 1.0~2.5μm spectral rang based on two types of material structures were investigated systematically. The first type InGaAs photodiode, marked by sample 1#, was fabricated using MOCVD epitaxial materials with P-i-N structure. The second type InGaAs photodiodes, marked by sample 2#, was fabricated using MBE epitaxial materials with P-i-N structure. The two types of photodiodes were fabricated by mesa etching technique, side-wall and surface passivation film. Dark current and voltage curves were measured by semiconductor parameters analyzer at different temperature, and dark current characteristics were analyzed using different perimeter to area method. The mechanism of the devices has been analysed. Polarization microscopy and conductive atomic force microscopy (c-AFM) have been used to investigate the local conductivity of the photodiodes’ sensitive area. Combining the optical and c-AFM micrographs with dark current characteristics, we intended to characterize the relationships of the leak current and the defect. The results indicate that sample 1# has relative much more leak defects than that of sample 2#, and thus the dark current sample 1# is higher than that of sample 2# and. The defects are generated at the body of material and spread to the surface, and these defects cause very high dark current of sample 1#.