Being known as a good environmental indicator, the anuran is an ideal animal model for investigating the quality of High Conservation Value (HCV) areas (fragmented forests) in maintaining or enhancing biodiversity values in an oil palm plantation. Using non-metric multidimensional scaling (NMDS) frogs from forest fragments and oil palm were investigated and compared, to identify species assemblages and guild. Our findings showed that species diversity differed significantly between High Conservation Values and the plantation areas. The High Conservation Value showed highest percentage of species endemism, and species of conservation importance in the areas. The NMDS analysis further suggests that the anuran assemblages at the oil palm plantation were disjunctive as the HCV areas provide isolated assemblages to the anuran species, different from that of the plantations. The number of species was found to be significantly influenced by water temperature, turbidity, salinity, and level of dissolved oxygen. Overall, the HCV areas supports high species diversity, including endemic and near threatened species compared to the plantation areas. Hence, these HCV areas are functioning and should be maintained as high priority areas for faunal conservation in an oil palm plantation.