GmILPA1 (Glyma.11g026400) is an important gene that controls petiole angle by modulating the formation of leaf pillow by promoting cell growth and division in soybean. The mutation of gmilpa1 can cause abnormal development of leaf pillow and increase petiole angle. However, whether the polymorphic variations of this gene in Soybean Germplasm determines the petiole angle remains unknown. In this study, re-sequencing data derived from 783 soybean germplasm accessions was used to analyze the haplotype variation of the GmILPA1 gene. Thirty-two polymorphic loci including 13 SNPs and 19 indels were detected, with a frequency of 1 SNP / 285 bp and 1 indel / 195 bp, respectively. Out of nine haplotypes, Hap1 was found to be predominant and Hap3 showed two non-synonymous mutations. The results showed that there were four α - helix differences in the secondary structure between Hap1 and Hap3, whereas there was not detected difference on the stimulated crystal structure. No significant difference in petiole angle among different haplotypes was observed. The number of polymorphic loci and haplotype diversity of GmILPA1 were decreased in varieties in relative to the landraces. Collectively, gained from the genetic diversity analysis, this study revealed a fixation (bottleneck) of GmILPA1 elite allele in varieties due to positive selection in the process of soybean breeding.