Wuyi Hongqu (WYH), also called black-skin-red-koji, which has been utilizing as a fermentation starter for more than one thousand years in China, is a symbiotic combination of Monascus spp. and Aspergillus niger formed through long-term application and domestication. In this study, the strains of Monascus purpureus and A. niger isolated from WYH samples were used to investigate their mutual influence, especially the effects on three main secondary metabolites from M. purpureus, Monascus pigments (MPs), monacolin K (MK), and citrinin (CIT), using a double-sided Petri dish (DSPD). The results showed that co-cultivation of M. purpureus and A. niger strains was favorable to increase the MPs production while inhibiting the CIT production by M. purpureus, especially when M. purpureus strains (M_1-1 or M₉) were co-cultivated with certain A. niger strains (An_1-2 or An₉), respectively, and both Monascus strains hardly produced detectable CIT. The expression levels of CIT-related genes in M. purpureus M_1-1 or M₉ were greatly restricted when co-cultivated with A. niger An_1-2 or An₉ confirmed by RT-qPCR. This study provides important insights into the selection of WYH production strains and the effects of fungal interactions.