One of the most effective atmospheric correction methods is dark-object subtraction (DOS) method, where the atmospheric offset can be generated from the image itself. The success of DOS strongly relies on the availability and quality of the dark target. Based on the response to the downwelling irradiances, the most effective dark target would be optically-deep water, which is not always available. It is important to assess the alternative dark targets in the absence of the ideal dark target. This research aimed at comparing the effectiveness of different dark targets for DOS method during mangrove above-ground carbon stock (AGC) mapping and comparing the accuracy with robust atmospheric correction FLAASH method. ALOS AVNIR-2 image was used as the test image, and mangrove forest of Karimunjawa and Kemujan Island was selected as the study area. The comparison covers the quality of healthy mangrove reflectance and the accuracy of vegetation indices for mangrove AGC mapping. The results of this research showed that non-ideal dark targets such as cloud-shadow pixels and the minimum value of the image can be used in the absence of ideal dark target, and DOS method is more efficient and effective than more robust atmospheric correction method.