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<i>Monascus</i> pigments (MPs) have been used as food colorants for several centuries in Asian countries and are currently used around the world via Asian catering. The MPs biosynthetic pathway has been well-illustrated; however, the functions of a few genes including <i>mrpigH</i> in the MPs gene cluster of <i>M. ruber</i> M7 are still unclear. In the current study, <i>mrpigH</i> was disrupted in Δ<i>mrlig4</i>Δ<i>mrpyrG</i>, a highly efficient gene modification system, using <i>mrpyrG</i> as a selection marker, and Δ<i>mrpigH</i>Δ<i>mrlig4</i>Δ<i>mrpyrG</i>::<i>mrpyrG</i> and Δ<i>mrpigH</i>Δ<i>mrlig4</i>Δ<i>mrpyrG</i> have been obtained. Subsequently, their morphologies, biomasses, MPs and citrinin (CIT) production were analyzed, respectively. These results have revealed that the deletion of <i>mrpigH</i> has significant effects on the morphology and growth of <i>M. ruber</i> M7. Moreover, compared with <i>M. ruber</i> M7, the yields of MPs and CIT were drastically increased and decreased in <i>mrpigH</i> mutants, respectively.