Gracilariopsis lemaneiformis is an important agarophyte,which is economically important.The industrialization of Gracilariopsis lemaneiformis started 20 years ago and has become one of the most important aquaculture in China.At present,the breeding of this species depends heavily on selective and other traditional breeding approaches.The molecular breeding system which is more efficient has not yet been established.The construction of genetic linkage map is urgent for the molecular marker assistant breeding and mapping of quantitative traits.Totally 400 pairs of SSR primers and 91 pairs of RSAP primer combinations were screened for parents of two mapping populations to provide polymorphic molecular markers for the construction of genetic linkage map.The genetic distances among four parents were evaluated.15 polymorphic markers between GL-F3 and GL-M8 and 8 polymorphic markers between GL-F6 and GL-M9 were obtained by SSR screening.88 polymorphic markers between GL-F3 and GL-M8 and 93 polymorphic markers between GL-F6 and GL-M9 were obtained by RSAP screening.The development of these markers set the basis for construction of genetic linkage map.The genetic distance revealed by SSR between GL-F3 and GL-M8 was 0.071 2,while that between GL-F6 and GL-M9 was 0.043 6 and the genetic distance revealed by RSAP between GL-F3 and GL-M8 was 0.228 4,while that between GL-F6 and GL-M9 was 0.253 7.The average covering loci and producing polymorphic of per primer combinations were much higher from RSAP than from SSR analysis,the RSAP is 4.48 times and 12.13 times of SSR between GL-F3 and GL-M8,respectively while it showed 5.81 times and 25.5 times between GL-F6 and GL-M9,respectively.RSAP markers were better than SSR in evaluating the genetic distance and genetic diversity of resources of G.lemaneiformis.The genetic difference among parents of mapping population of G.lemaneiformis was proved.The development of SSR and RSAP markers set a foundation for the construction of genetic linkage map.The study revealed low genetic diversity in this species and other approaches,such as mutagenesis,cell engineering and transgenic were suggested to be exploited in further breeding attempts.