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Ramie (Boehmeria nivea L. Gaudich) is a major natural fiber crop cultivated in East Asia. The improvement of its fiber yield and fineness are important breeding goals. Fiber yield is a complex quantitative trait comprising ramet number, stem diameter, plant height, skin thickness, and fiber percentage. The fiber fineness is a crucial trait for ramie fiber quality. However, there are few association studies for fiber yield traits and fiber fineness on ramie, and lack high-density SNP maps in natural ramie population. Here, a panel of 112 core ramie germplasms were genotyped by 215,376 consistent single-nucleotide polymorphisms (SNPs) from specific-locus amplified-fragment sequencing (SLAF-seq), and used for genome-wide association study of fiber fineness and yield. Subsequently, the genetic diversity, linkage disequilibrium (LD), and population structure was conducted based on 215,376 SNPs. Population cluster analysis disclosed five subpopulations. Neighbor-joining (NJ) analysis revealed three major clusters. No obvious relationships were identified between them and their geographic origins. The genome-wide LD decayed to r2 = 0.1 was ~ 11.75 kbp in physical distance. One, seven, one, seven, and twenty-seven significant SNP marker associations were detected for fiber fineness (third season), stem diameter (third season), stem skin thickness (third season), fiber percentage (second season), and fiber percentage (third season), respectively. Two promising candidate genes, whole_GLEAN_10029622 and whole_GLEAN_10029638 resided in the significant trait-SNP association for fiber fineness (third season), which annotated as a cotton fiber-expressed protein and an Arabidopsis thaliana homebox protein ATH1, respectively and validated by qPCR. The identified loci or genes for fiber fineness and yield may provide the basis for future research on fiber fineness and yield and marker-assisted selection breeding for ramie. [ABSTRACT FROM AUTHOR]