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Imagery classification has long been used in analyzing remote sensing data. The use of the classification algorithm model can affect the results in interpreting benthic habitats in shallow water. This study aimed to determine the best classification algorithm model for mapping benthic habitat cover through Sentinel-2 satellite imagery. Three algorithm models were employed: Maximum Likelihood Classification (MLC), Minimum Distance Classification (MDC), and Mahalanobis Distance Classification (MaDC). The benthic habitat types were extracted using Lyzenga correction, giving three categories: coral, seagrass, and sand. The results showed that the application algorithm models of the MLC, MDC, and MaDC on the benthic habitat mapping resulted in an accuracy value that was not significantly different at the 95% confidence interval. However, of the three algorithms used, the MaDC algorithm provides the best results in overall accuracy (78.35%) than the MDC (74.45%) and the MLC (74.33%). It shows that the MaDC algorithm can be referred to as the mapped benthic habitat cover in the Kei Islands. However, this algorithm model needs to be continuously studied and compared to other models in other locations. [ABSTRACT FROM AUTHOR]