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.