This study investigates the variations in benthic diatom assemblages across a salinity gradient in Mai pond, a brackish environment located on Jeju Island, South Korea. Brackish zones are ecologically important regions where freshwater and seawater mix, creating a dynamic transition zone which supports diverse habitats and species. Benthic diatoms, a group of photosynthetic microalgae, play a crucial role in estuarine ecosystems by serving as primary producers and indicators of environmental changes. The primary objective of this research is to examine how salinity gradients influence the composition and distribution of benthic diatom communities in Mai pond. To achieve this, water and sediment samples were collected along a transect spanning the brackish zone, covering a range of salinity levels. Diatom species were identified and quantified using Light microscopic and Scanning electron microscope, allowing for a comprehensive analysis of community structure and diversity. Microscopic observations have been revealed distinct variations in benthic diatom assemblages corresponding to the salinity gradient. Certain species exhibited preferences for either freshwater or marine environments, while others demonstrated a greater tolerance for salinity fluctuations. These findings highlight the ecological significance of salinity gradients in shaping the distribution and composition of benthic diatoms in Mai pond. Understanding the responses of benthic diatom communities to salinity gradients in brackish ecosystems contributes to our knowledge of the overall brackish biodiversity and functioning. Moreover, the present research would provide valuable insights for the conservation and management of brackish environments, particularly in the context of ongoing global environmental changes and their potential impacts on coastal ecosystems.