The mating-type locus of Chlamydomonas reinhardtii exists as two apparent alleles (mt+ and mt-) that control mating in haploid gametes and sporulation and meiosis in diploid mt+/mt- zygotes. Twelve genes, seven unrelated to life cycle transitions, are tightly linked to mt, suggesting that the locus exerts recombinational suppression. A 1.1 Mb chromosome walk from a gene linked to mt demonstrates that the mt+ and mt- loci carry four intrachromosomal translocations, two inversions, and large deletions and duplications within a 190 kb sector, presumably accounting for the recombinational suppression that extends through 640 kb of flanking homologous DNA. The rearranged domain also carries blocks of mt(+)- and mt(-)-specific sequences, at least one of which includes a mt(+)-specific gene. The locus has the properties of an incipient sex chromosome.