Abstract: In order to explore the important lncRNA and its target genes in the asymmetric development of female chicken embryo’s gonads, the gonads on both sides of female chicken embryo at E9 stage were taken as the research object in the experiment. The transcriptome sequencing（RNA-seq） technology and bioinformatics methods were used to analyze and predict the lncRNAs of the left and right gonads of female chicken embryos. And the DESeq2 v1.30.1 software was used to identify the differential expression mRNAs and lncRNAs between the gonads of both sides. The cis and trans target genes of differential expression lncRNAs were predicted. GO functional annotation and KEGG enrichment analysis on the target genes were performed. The expressions of important target genes were verified through quantitative real-time PCR（qRT-PCR）. The results showed that 653 intergenic lncRNAs, 467 intronic lncRNAs, and 1339 antisense lncRNAs were predicted by RNA-seq. There were 1856 differential expression mRNAs and 443 differential expression lncRNAs between the left and right gonads of female chicken embryos. 229 genes including GRIA1, DIO3, FSHR, LHX9, CYP17A1, and TOX3 were found to be target genes for differential expression lncRNAs. The differential expression lncRNAs’ target genes in both gonads were mainly enriched in steroid metabolism, positive regulation of intracellular estrogen receptor signaling pathways, and metabolic pathways. The expression of mRNAs confirmed by quantitative real-time PCR was basically consistent with the results of RNA-seq. These results indicated that the left and right gonads of female chicken embryos had different levels of expression and specific expression of mRNAs and lncRNAs, which might affect the asymmetric development of the left and right gonads of female chicken embryos.