Efffcts of physico-chemical factors on the zonation and vertical distribution of benthic microalgal communities in the tidal flats of Youngkwang and Canaiin, Korea, were studied. Concentrations of nutrients were low throughout the study period. A 38 species of benthic microaigae was identified. Most of the algae were pennate diatoms with small size. Cell numbers at silty sediments were higher than sandy sediments, and showed high patchy distribution. Zonal distributions of benthic microalgae showed higher variation from silty sediment than sandy sediments. Benthic microalgae showed vertical migration within the upper few mm of sediment with periodicity closely related to tidal cycles. Maximum cells were observed from 0 mm depth both sandy and silty sediments. Cells of benthic microalgae in the 1 - 2 mm depth decreased after desiccation of sediments. The variation of cells was higher at sandy sediments than silty sediments. Cell numbers of benthic microalgae showed no positive relationships with pH and nutrinets except NH$_4$-N.