SUMMARYDominance of one phase (i.e. diploid or haploid) has been reported in various isomorphic macroalgae; however, studies of the relative frequencies of the two phases are limited to a few taxa owing to the difficulty in identifying phases of sterile thalli. In Dictyota dichotoma, we have previously documented the dominance of fertile sporophytes. In the present study, the phase and sex ratios of sterile thalli of D. dichotoma were determined using newly developed sex‐specific markers. Differentially expressed genes were detected by transcriptome analyses of female and male gametophytic strains and a sporophytic strain aiming to identify candidate sex‐specific genes. These candidates were aligned with genome sequences on the sex chromosomes of Ectocarpus siliculosus and were identified as putative sex‐specific genes of D. dichotoma. Two primer sets were designed to discriminate phase and sex by the presence or absence of PCR products, and these markers were applied to examine the phase and sex ratios of D. dichotoma in various habitats and seasons. The proportion of sporophytes against 33–50 thalli examined in each of the five habitats at Ebisu Island, Shizuoka Prefecture was 88–100%, and the proportion of fertile sporophytes against total sporophytes (fertility proportion) varied among the habitats (0–54%). The fertile sporophytes were remarkably larger than the sterile sporophytes. At Tateyama, Chiba Prefecture, the dominance of sporophytes occurred in all seasons. The fertility proportion of sporophyte was relatively high from February (62.4%) to May (91.9%) and lower than 23% in other seasons. When artificial substrates were anchored in the middle of the D. dichotoma population, newly recruited thalli were all sporophytes, suggesting infrequent reproduction via tetraspores in nature. Based on these findings, we discuss potential fitness differences between the phases of D. dichotoma.