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Continuous and intensive selective breeding reduces the genetic diversity of cultivated  Pyropia  stock, thereby increasing its susceptibility to diseases, and hindering the sustainable development of the  Pyropia  industry. To develop new  Pyropia  germplasms with desirable agronomic traits, a new  Pyropia yezoensis  strain, “Huangyou No. 1” was bred from a wild subtidal population. In this study, the genetic diversity of this strain was analyzed using AFLP. Totally, 249 loci were obtained, of which 248 were polymorphic with a polymorphism rate of 99.6%, using seven primer pairs. The intra-population polymorphism rates of the populations Wild 1 and Wild 2 were the highest (47.39% and 59.44%, respectively), while they were relatively low (20.88–24.5%) in the cultivated populations. The genetic distances between the breeding  Pyropia  populations cultivated in the same aquaculture farm were low. Specifically, the F 2  offspring of “Huangyou No. 1” and the control cultivar, cultivated using the “never-drying” protocol, were genetically distant from the other populations, including that from the same seedlings, yet cultivated using the “periodic-drying” protocol. The never-drying cultivation protocol had a high likelihood of influencing genetic diversity of  Pyropia yezoensis .

AFLP fingerprints of Pyropia yezoensis (Bangiales, Rhodophyta) populations revealed the important effect of farming protocols on genetic diversity