[Background] Lactobacillus paraplantarum L-ZS9, which could produce bacteriocin, would be used in food preservative and fermentation. [Objective] To understand expression characters of regulated genes of bacteriocin synthesis under environment stress conditions for Lactobacillus paraplantarum L-ZS9. [Methods] We used high-throughput sequencing technology to sequence its transcriptome. Based on the Clusters of Orthologous Groups (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, we carried out functional annotation and classification, pathway annotation. [Results] The results suggested that distribution of genes’ coverage is beyond 90% of two samples, the total genes with expression difference were 927, of which 744 were up regulation and 183 down regulation. KEGG pathway analysis showed that 68 out of the 649 genes with different expression levels were classed into ABC transport pathway, accounting for 10.48% and three genes were up regulated beyond 16 times and one was down regulated beyond 1/16. In addition, expression of some orphan genes changed with 16 times up or down-regulation, some even could increase more than 10 000 times. [Conclusion] This study further improved the gene information and laid the foundation of bacteriocin metabolic pathway and stress respond research for Lactobacillus paraplantarum.