Pigmentation-related mutations may be used to distinguish between differentially colored sectors of chimeric thalli, which may lead to the efficient breeding of economically valuable Pyropia/Porphyra seaweed species. However, the quantitative trait loci and alleles underlying Pyropia/Porphyra coloration remain unidentified, thereby limiting the utility of coloration mutants for breeding and genetic analyses. In this study, to maintain the integrity of the genetic structure of the population, only four-colored thalli were considered when constructing the doubled haploid (DH) Pyropia haitanensis population comprising 480 homozygous offspring lines (i.e., the largest DH Pyropia/Porphyra population). The offspring lines in the DH population had wild-type colored and orange sectors the segregation ratio of the two types of coloration was nearly 1:1, indicating the orange coloration was controlled by a single nuclear gene. A 0.5 Mb candidate region was identified in the P. haitanensis genome on the basis of a BSA-seq analysis (99% confidence interval). Furthermore, a non-synonymous SNP [A/G] was detected in the coding region (base-pair position 481) of PhcpcC, which encodes a phycocyanin-associated rod linker protein. This SNP locus was verified in DH and natural populations. More specifically, the base at this locus was A in the wild-type colored lines and G in the orange lines. Hence, PhcpcC may be the gene associated with the orange coloration of P. haitanensis. The molecular marker developed in this study may be used to exploit pigmentation mutants for breeding and genetic analyses of Pyropia/Porphyra species.