The common carp, a gonochoristic teleost fish with an XX/XY sex-determining system, provides an excellent model for studying cyprinidae gonadal sex differentiation. The present study aims at investigating the detailed process of early gonadal sex differentiation of common carp by combining the expression patterns of sex related genes (cyp19a1a, foxl2, amh, dmrtl1 sox9b, sycp3, dmc1) with gonadal histological changes using mono-sex female and male Yellow River carp. H&E staining, immunohistochemistry and immunofluorescence of gonads indicated that the ovaries and testis of common carp were both directly differentiated from undifferentiated gonads. Oogonia and spermatogonia were first observed at 40 dph (days post hatching) and 70 dph in female and male gonads, respectively. Female related genes cyp19a1a and foxl2 and male related genes amh, dmrt1 and sox9b increased significantly in 30-40 dph female, and male gonads, respectively. These suggest that the critical timing of sex determination of common carp takes place between 30 and 40 dph or possibly earlier. Meiotic marker gene dmc1 and sycp3 increased expression significantly in 55 dph female gonads while sycp3 increased expression significantly in 100 dph male gonads. Oocytes in meiosis and spermatocytes were first observed in 55 dph female and 100 dph male gonads, respectively. These indicate that the initiation time of gonadal sex differentiation is 50-55 dph in female common carp and 90-100 dph in male common carp. To our knowledge, this is the first study investigating the detailed process of early gonadal sex differentiation of common carp by combining the expression patterns of sex related genes with gonadal histological changes. We have identified the critical window of sex determination and the initiation times of oogenesis and spermatogenesis in the Yellow River carp. These results provide researchers with valuable information to possibly reveal the mechanisms of sex determination and differentiation of common carp.