Monascus pigments have been used as natural food colorants in Asia for centuries. They are not authorized for use in the European Union and the United States mainly due to the risk of coproduction of the mycotoxin citrinin by Monascus slop. In the present study, we screened for novel producers of Monascus-like pigments from ascomycetous filamentous fungi belonging to Penicillium subgenus Biverticillium that are not reported to produce citrinin or any other known mycotoxins. The screening was carried out using the X-hitting algorithm as a tool to quickly screen through chromatographic sample data files of 22 different Penicillium extracts with 12 Monascus pigment extracts as controls. The algorithm searched for the most similar UV-vis spectra of the metabolites (cross hits) present in the pigment extracts to those of the selected reference metabolites viz. monascin, rubropunctatin, rubropunctamine, and citrinin. The cross hits were then manually identified on the basis of their UV-vis and mass spectra. X-hitting was found to be a good tool in the rapid screening of crude pigment extracts. Monascus pigments were discovered in the extracts of two closely related species of Penicillium that were only distantly related to the genus Monascus. Monascorubrin, xanthomonasin A, and threonine derivatives of rubropunctatin were identified in the extract of Penicillium aculeatum IBT 14263, and monascorubrin was identified in the extract of Penicillium pinophilum IBT 13104. None of the tested Penicillium extracts showed the presence of citrinin. Thus, the present study brought out two novel promising sources of yellow, orange, and purple-red Monascus-like food pigments in the species of Penicillia that do not produce citrinin and opened the door to look for several more new promising sources of natural food colorants in the species of Penicillia.