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Background   Lactobacillus plantarum  is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food. In the present study, the genetic diversity and population structure within 186  L. plantarum  isolates was determined based on a novel MLST scheme employing eight housekeeping genes. These isolates had originated from different sources and geographic regions: 179 isolates were from our own culture collection and originated from China and Mongolia and seven isolates were type or reference isolates from other collections.    Results  The results showed that 179 isolates and seven reference isolates could be assigned to 73 different sequence types (STs), forming ten clonal complexes (CCs) and 23 singletons. There were 158 polymorphic sites detected in total, and the nucleotide diversity per site varied from 0.00401 in  clpX  to 0.03220 in  groEL . The minimum spanning tree analyses suggested that the evolution of  L. plantarum  isolates have little relationship with ecological sources have similar nucleotide diversity. Phylogenetic trees and structure indicated that there were six lineages in the  L. plantarum  isolates used in our study. Split-decomposition and ClonalFrame analysis indicated that recombination had occurred throughout the population of  L. plantarum , but it occurred at a low frequency in these eight loci.    Conclusion  We deduced that  L. plantarum  isolates from the same ecological niches have similar genetic diversity and population structure. The MLST scheme presented in this study provides abundant sequence data for  L. plantarum  and enabled global comparisons of isolates associated with various environmental origins to be made. This will further advance our understanding of the microbial ecology of this industrially important LAB.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-015-0584-4) contains supplementary material, which is available to authorized users.

Use of multilocus sequence typing to infer genetic diversity and population structure of Lactobacillus plantarum isolates from different sources