[Objective] The effect of continuous low-expression region on validamycin A titer and biomass was evaluated through gene deletion experiments.[Methods] The deletion boundaries of large chromosome region were identified via transcriptome analysis. Meanwhile, deletion mutant was obtained via Cre-loxP system, titer of validamycin A was detected by HPLC and, biomass was represented by dry cell weight.[Results] The 1.2 Mb large region identified via transcriptome analysis was successfully deleted by Cre-loxP system. In comparison with parent strain TL01, deletion of 1.2 Mb region increased the biomass by 44% and showed no effect on validamycin A titer.[Conclusion] The strategy developed here can be applied to identify deletion boundaries of large chromosome region, and mutant of 1.2 Mb region deletion showed potential as host for heterologous expression of aminocyclitol biosynthetic gene clusters.