Angiopteris fokiensis is an endangered fern with ecological and medicinal value, yet genetic studies to support its conservation have been scarce. We performed a genome survey using high-throughput sequencing, developed genomic SSR markers from a draft assembly, and genotyped 96 individuals from 10 populations in Guangdong Province. The genome size was ~4.44 Gb (1.89% heterozygosity). From a 3.58 Gb contig assembly, 4,327,181 SSR loci were identified, with 15 highly polymorphic SSR markers being developed. Genotyping showed high within-population genetic diversity, low inter-population differentiation, and 98.55% of variation within populations. Bayesian structure, principal coordinates analysis, and neighbor-joining tree analyses consistently indicated admixed genetic clusters without clear geographical division. Additionally, the analysis revealed no significant correlation between genetic and geographic distances. Conservation should prioritize intra-population diversity via in situ/ex situ strategies. This study provides the first genomic SSR resources for A. fokiensis and underscores the importance of conserving within-population genetic diversity through integrated in situ and ex situ strategies.

Globba spp. is a perennial herbaceous plant of the Zingiberaceae family, characterized by its unique floral architecture and diverse coloration with high ornamental and medicinal value. However, research on the genetic basis of Globba is still insufficient, and only a limited number of molecular markers have been developed so far, which has greatly hampered the progress of its molecular breeding. Herein, we performed the first deep identification of genome-wide SSR markers based on the whole-genome data of G. sherwoodiana. A total of 276,809 SSR loci were identified with an average density of 189.24–297.49 SSRs/Mb within each chromosome. Mononucleotide repeat loci were most abundant, accounting for 58.95% of all SSRs, with dinucleotide and trinucleotide repeats accounting for 19.83% and 19.27%, respectively. Using G. sherwoodiana ‘MJ16’ and G. winitii C.H. Wright as parental lines, we constructed a hybrid F₁ population containing 173 individual plants. The coefficient of variation (CV) of the 10 phenotypic traits ranged from 13.09% to 27.43%, exhibiting a normal distribution. Phenotypic traits including terminal leaf width, inflorescence length, inflorescence width, secondary-inflorescence pedicel length, number of ornamental bracts, and basal inflorescence-bract length showed abundant variation, with all CV values exceeding 20%. Moreover, 27 polymorphic genomic SSRs (gSSR) were screened from the synthesized 192 primer pairs, amplifying a total of 203 alleles. On average, each marker detected 7.52 polymorphic loci, with a mean effective allele number of 3.63 and a mean polymorphism information content of 0.64, reflecting a relatively rich genetic diversity within the population. Through phenotype–marker association analysis, six gSSR loci were found to be significantly associated with six phenotypic traits. The highest interpretation ratio (16.86%) was observed for basal inflorescence-bract width. Three loci (gSSR48, gSSR105 and gSSR184) were simultaneously associated with more than two phenotypic traits, indicating a pattern consistent with pleiotropy or linkage. The informative gSSR markers and the association analysis results in this study provide an effective theoretical basis for germplasm identification, genetic diversity evaluation, and marker-assisted breeding of Globba.