Great progresses have been made to carry out Fenton oxidation under neutral or alkaline pH in which, nevertheless, organic acids and other acidic intermediates usually result in acidic Fenton effluent. To eliminate the classical neutralization step prior to biological treatment, acid-tolerant microbes were here screened and used for purification of acidic Fenton effluent to achieve pH increase and further COD (chemical oxygen demand) removal. The bacterial and fungal community diversity was analyzed before and after screening for acid-tolerant microbes. After screening the bacterial diversity sharply decreased while the fungal diversity at the genus level became richer, mainly including Phialemoniopsis (relative abundance 38.69%), Vanrija (20.08%), Hypocreaceae (18.44%) and Candida (14.74%). Acidic pH and residual H