BackgroundUnderstanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs.MethodsIn this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species,Geodorum eulophioides(endemic and endangered in Southwest China), and a widespread species,G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level.ResultsThe results showed that the nucleotide diversity and heterozygosity ofG. eulophioideswere significantly higher than those ofG. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a fewG. eulophioidesindividuals were detected with genetic components fromG. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat ofG. eulophioidesinvasion byG. densiflorumunder anthropogenic disturbance may be the main factor causing interspecific hybridization.ConclusionsTherefore, reducing or avoiding habitat disturbance is a key measure to protect theG. eulophioidespopulations. This study provides valuable information for future conservation programs for narrowly distributed species.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04285-w.