Porphyra haitanensis is a unique seaweed species that grows in South China and has the highest production (by weight) in Chinese aquaculture. However it has been a great loss in nori farming due to the degeneration of the germplasm quality in the last years. In order to understand the genetic bakground of P. haitanensis and guide its genetic breeding and germplasm resource protection, Inter-simple sequence repeats (ISSR) markers were used to investigate the genetic variations within and among 3 populations (PT, NR and DS) of P. haitanensis. The thalli samples were collected from 60 individuals. 15 ISSR primers gave rise to 222 discernible DNA bands of which 186 (83.78%) were polymorphic, indicating a considerable genetic variation at specific level. At the population level, the percentage of polymorphic bands (P) was from 80.18% to 81.53%, 80.93% on average. Expected heterozygosity (h) and Shannon’s information index (I) were 0.3304 and 0.4834 respectively at specific level, 0.3809 and 0.4551 at population level. According to the value of G_st, a large proportion of genetic variance (93.5%) of P. haitanensis was among individuals within population, only 6.5% genetic variance was among populations, the results indicated that the genetic differentiation level among the 3 populations of P. haitanensis was low. And according to the value of N_m, the reason of the low genetic differentiation level among populations of P. haitanensis was the sufficient gene flow. UPGMA cluster analysis based on Nei’s genetic distance showed that the individuals from the same population were no grouped together, but randomly. At Last, the necessary of protecting the germplasm resource of P. haitanensis also was discussed.