Monascus　spp.　and　its　secondary　metabolites　have　been　widely　applied　in　foods　and　medicines　for　thousands　of　years　in　eastern　Asia.　Nitrogen　sources　are　essential　nutrients　for　the　growth　and　metabolism　of　Monascus　spp.　Our　previous　study　found　that　inorganic　nitrogen　sources　(especially　NH4Cl　and　NH4NO3)　promoted　the　biosynthesis　of　Monascus　pigments　(MPs)　and　inhibited　the　production　of　citrinin.　The　objective　of　the　present　study　was　to　investigate　the　regulatory　mechanism　of　inorganic　nitrogen　on　the　biosynthesis　of　MPs　and　citrinin　by　the　comparative　transcriptional　approach　(RNA　sequencing　combined　with　RT-qPCR).　Results　indicated　that　the　submerged　fermentation　of　M.　purpureus　M3103　with　NH4Cl　or　NH4NO3　as　the　sole　nitrogen　source　can　significantly　increase　the　yields　of　MPs　(especially　for　Monascus　orange　and　red　pigments)　and　decrease　citrinin　production,　compared　with　the　organic　nitrogen　source　(peptone　group).　Comparative　transcriptomic　profiling　by　RNA　sequencing　found　that　the　numbers　of　differentially　expressed　genes　(DEGs)　between　different　experimental　groups-M　group　(peptone　group)　vs.　ML　group　(NH4Cl　group),　and　M　group　(peptone　group)　vs.　MX　group　(NH4NO3　group),　were　722　and　1287,　respectively.　Kyoto　Encyclopedia　of　Genes　and　Genomes　(KEGG)　pathway　analysis　revealed　that　genes　involved　in　carbon　and　nitrogen　metabolism,　biosynthesis　of　amino　acids　were　up-regulated　by　NH4Cl　and　NH4NO3,　which　would　produce　more　biosynthetic　precursors　for　MPs.　Whereas,　the　inorganic　nitrogen　source　(both　of　NH4Cl　and　NH4NO3)　down-regulated　the　expression　levels　of　genes　involved　in　tyrosine　metabolism.　In　addition,　NR　analysis　indicated　that　the　essential　genes　and　transcription　factors　involved　in　the　biosynthesis　pathway　of　citrinin　were　down-regulated　by　NH4Cl　and　NH4NO3.　These　results　indicated　that　NH4Cl　or　NH4NO3　as　a　nitrogen　source　for　M.　purpureus　M3103　can　significantly　promote　the　precursor　synthesis　of　Monascus　pigments,　but　reduce　the　transcription　of　polyketide　synthase　for　citrinin,　and　therefore　significantly　increase　Monascus　pigments　production　and　decrease　citrinin　formation.　These　findings　will　facilitate　a　comprehensive　understanding　of　the　regulatory　mechanisms　of　inorganic　nitrogen　in　the　biosynthesis　of　secondary　metabolites　in　M.　purpureus,　and　would　benefit　the　application　of　M.　purpureus　in　the　production　of　MPs.