Abstract:In order to explore the genetic differences between the traditional and new strains(SW-81,HR-5) of Neoporphyra haitanensis in Dongtou district,Wenzhou,the genetic diversity of 60 individuals in these three strains was studied using CO I and rbcL gene fragments.After comparative analysis,the 398 bp CO I gene sequence and 488 bp rbcL gene sequence were obtained with an isologous sequence,the joint analysis length was 886 bp,and the content of T,C,A and G in all obtained sequences was 35.100%,14.220%,34.320% and 16.360%,respectively.There were 6 mutation sites,including 5 single mutation sites and 1 simple information site;The nucleotide diversity of the three strains was 0.000 30±0.001,and the haplotype diversity was 0.249±0.074.60 individuals defined 6 haplotypes,and Hap3 was the core haplotype,accounting for 88.600% of all individuals,respectively;The haplotype-constructed NJ phylogenetic tree showed that there was gene communication in each strain,and genetic differentiation had not yet occurred.The results showed that the genetic diversity of the new strain of N. haitanensis was low,so the scope of germplasm protection and breeding should be improved to prevent germplasm degradation.It is recommended to use multiple strains in the production process of seaweed seedlings to adapt to the changing marine environment.