Effective analytical approaches for the identification of natural dyes in historical textiles are mainly based on high-performance liquid chromatography coupled with spectrophotometric detection and tandem mass spectrometric detection with electrospray ionization (HPLC-UV-Vis-ESI MS/MS). Due to the wide variety of dyes, the developed method should include an adequate number of reference color compounds, but not all of them are commercially available. Thus, the present study was focused on extending of the universal analytical HPLC-UV-Vis-ESI MS/MS approach to commercially unavailable markers of red, purple, and blue dyes. In the present study, HPLC-UV-Vis-ESI MS/MS was used to characterize the colorants in ten natural dyes (American cochineal, brazilwood, indigo, kermes, lac dye, logwood, madder, orchil, Polish cochineal, and sandalwood) and, hence, to extend the analytical method for the identification of natural dyes used in historical objects to new compounds. Dye markers were identified mostly on the basis of triple quadrupole MS/MS spectra. In consequence, the HPLC-UV-Vis-ESI MS/MS method with dynamic multiple reaction monitoring (dMRM) was extended to the next 49 commercially unavailable colorants (anthraquinones and flavonoids) in negative ion mode and to 11 (indigoids and orceins) in positive ion mode. These include protosappanin B, protosappanin E, erythrolaccin, deoxyerythrolaccin, nordamnacanthal, lucidin, santalin A, santalin B, santarubin A, and many others. Moreover, high-resolution QToF MS data led to the establishment of the complex fragmentation pathways of α-, β-, and γ- aminoorceins, hydroxyorceins, and aminoorceinimines extracted from wool dyed with Roccella tinctoria DC. The developed approach has been tested in the identification of natural dyes used in 223 red, purple, and blue fibers from 15th- to 17th-century silk textiles. These European and Near Eastern textiles have been used in vestments from the collections of twenty Krakow churches.