The gametes of chlorophytes differ morphologically even in isogamy and are divided into two types (α and β) based on the mating type- or sex-specific asymmetric positioning of the mating structure (cell fusion apparatus) with respect to the flagellar beat plane and eyespot, irrespective of the difference in gamete size. However, the relationship between this morphological trait and the mating type or sex determination system is unclear. Using mating type-reversed strains of the isogamous alga Chlamydomonas reinhardtii, produced by deletion or introduction of the mating type-determining gene MID, we revealed that the positioning of the mating structure is associated with conversion of mating types (mt– and mt+), implying that this trait is regulated by MID. Moreover, the dominant mating type is associated with the type β phenotype, as in the chlorophyte species Ulva prolifera. Our findings may provide a genetic basis for mating type- or sex-specific asymmetric positioning of the chlorophyte mating structure.