Hongqu　is　a　product　fermented　by　Monascus.　To　improve　the　quality　of　Hongqu,　isolation　and　identification　of　high-quality　Monascus　strains　are　required,　but　the　current　identification　scheme　of　Monascus　and　the　screening　strategy　of　high-quality　strains　are　still　insufficient.　For　this　purpose,　based　on　the　construction　of　the　Monascus　strain　library,　the　results　of　morphological　identification　and　molecular　biological　identification　of　Monascus　were　compared,　and　a　reasonable　identification　scheme　was　proposed　through　correlation　analysis;　the　yield　of　pigment　and　citrinin　were　determined　for　strains　with　different　morphological　types,　and　high　-quality　Monascus　strains　were　screened　by　yield　conversion　method.　Result:　Multiple　Monascus　strains　with　different　morphologies　may　exist　in　a　single　Hong　Qu,　and　a　Monascus　strain　bank　was　constructed　containing　45　different　morphological　typing　isolates　for　a　total　of　148　Monascus　spp.　with　44　Hongqu　samples　as　the　source　of　strains;　Morphological　analysis　indicated　that　most　Monascus　spp.　were　similar　to　M.　purpureus,　M.　aurantiacus,　and　M.　pilosus,　while　ITS　rDNA　sequencing　and　18S　rDNA　sequencing　easily　matched　unknown　Monascus　spp.　to　M.　purpureus,　M.　pilosus,　and　M.　ruber;　correlation　analysis　indicated　that　ITS　rDNA　sequencing　more　closely　resembled　the　morphological　analysis　results　than　18S　rDNA　sequencing;　due　to　the　larger　variety　and　number　of　reference　strains　in　gene　databases　for　ITS　rDNA　sequencing,　ITS　rDNA　sequencing　result　is　recommended　when　the　results　are　different　among　multiple　identification　methods;　at　last,　Monascus　MZT27　with　high-yield　pigment　(83.3　U/mL)　and　low-yield　citrinin　(81.5　ng/mL)　was　screened　by　referring　to　the　three　indexes　of　pigment　yield,　citrinin　yield,　and　the　ratio　of　citrinin　yield　to　pigment　yield,　and　Monascus　MZT39　with　high-yield　yellow　pigment　(accounted　for　70.06%)　was　screened　by　the　ratio　of　yellow　to　total　pigment.　This　study　contributes　to　the　exploitation　of　Monascus　germplasm　and　the　promotion　of　the　quality　of　Hongqu.　©　2023　Chinese　Institute　of　Food　Science　and　Technology.　All　rights　reserved.