The characterization and expression of Sox4 in large yellow croaker (Lc-Sox4) were studied in this paper. Lc-Sox4 contains a protein of 371 amino acids with a conserved high mobility group box. Quantitative real-time PCR displayed that the expression of Lc-Sox4 had tissue and gender specificity existing in brain, gonad, heart, intestine, and head kidney with male>female, in eye with female>male. During embryogenesis, Lc-Sox4 was expressed highest in one-day-post-hatching stage, next in formation-of-eye-lens stage. The expression pattern of Lc-Sox4 was different from that of Lc-Sox11a. The expression of Lc-Sox4 was significantly lower than that of Lc-Sox11a in the all tested tissues and embryonic stages except in heart, spleen, mutiple-cell, formation-of-eye-lens, and one-day-post-hatching stages (with Lc-Sox4 higher than Lc-Sox11a). There was overlapping expression between Lc-Sox4 and Lc-Sox11a in brain, gill, female eye, testis, formation-of-eye-lens stage and one-day post hatching stage. The whole mount in situ hybridization results indicated that Lc-Sox4 was expressed at all embryonic stages except 2-cell stage. The positive signals were mainly distributed in the central nervous system and notochord at one-day-post-hatching stage. In short, we first identified and analyzed the temporal and spatial expression patterns of Lc-Sox4 to elucidate its important influence on the development of nervous system, visual system and heart. We also detected the overlapping expression between Lc-Sox4 and Lc-Sox11a which may reveal the functional redundancy of them. These data would shed light on the molecular mechanism of development in large yellow croaker.