For clarifying the difference of genetic diversity and linkage disequilibrium (LD) level between cultivated (Glycine max (L.) Merr.) and annual wild soybean (Glycine soja Sieb. & Zucc.), genetic variation pattern of 8 SNP loci developed from soybean cyst nematode resistance candidate genes rhg1 and Rhg4 in soybean germplasm were analyzed. The results indicated that G. max population, consisted of cultivated soybean mini-core collection and modern cultivars, had a higher LD levels (R2 value is 0.216) than G. soja population. Since 100% of pairwise loci within a gene and 16.6% of pairwise loci between genes were significant in G. max population, two specific LD regions were formed for each gene. A total of 46 haplotypes were detected in 363 soybean germplasm. The population of G. soja had less number of haplotypes and higher haplotype diversity than the population of G. max. Among the 31 population-specific haplotypes, 15 haplotypes were specific for G. soja population. In addition, the frequency of two major predominant haplotypes (Hap_10 and Hap_11) in G. soja population was obviously decreased in G. max population, which might indicate that some new haplotypes were formed and some old haplotypes were lost during the G. max domesticated from G. soja.