Lmx1b is a LIM-homeodomain transcription factor, which still express in corneal endothelium and stroma at least to postnatal day 40.Although putative Lmx1b target genes have been identified, the downstream targets of it in mouse corneal stroma and endothelium are still unknown.To identify genes targeted by Lmx1b, we compared transcriptome data from Lmx1b silenced and wild cell types.54 and 50 target genes were differentially expressed in mouse corneal endothelial cells and stromal cells.Several corneal targets, including PAX-6, PITX2 and TIGR, demonstrated an increase of expression in the Lmx1b silenced cell types, suggests a mechanism that includes changes in these compositions to contribute to elevated intraocular pressure or even glaucoma.Our study provides the most comprehensive characterization of genes regulated by Lmxlb in mouse corneal endothelial cells and stromal cells and lays the ground work for further investigation of glaucoma in molecular genetics.