The frequency, type and distribution of simple sequence repeats (SSRs) in Porphyra haitanensis genomes was investigated using expressed sequence tag (EST) data deposited in public databases. A total of 3,489 non-redundant P. haitanensis ESTs were screened for SSRs using SSRhunter software. From those, 224 SSRs in 210 ESTs were identified; trinucleotides were the most common type of SSR (64.29%), followed by dinucleotides (33.48%). Tetranucleotides, pentanucleotides, and hexanucleotides were not common. Among all identified motif types, CGG/CCG had the highest frequency (33.9%), followed by TC/AG (24.6%). From these EST-SSRs, 37 SSR primer-pairs were designed and tested using common SSR reaction conditions with 15 P. haitanensis DNAs as templates. The results showed that 28 SSR primer-pairs gave good amplification patterns. These were used to conduct SSR analyses of genetic variations of the 15 germplasm strains of P. haitanensis. A total of 224 alleles were detected, with the number of alleles ranging from 4 to 15. The effective number of alleles, expected heterozygosity, and polymorphism information content of the 15 germplasm strains of P. haitanensis were 2.81, 0.64, and 0.57, respectively. All of these parameters indicate that the 15 germplasm strains of P. haitanensis harbor rich genetic variation.