Along with the known kaempferol-3-O-alpha-l-rhamnopyranosyl-(1 -> 2)-[6-O-(3-hydroxy-3-methylglutaryl)]-beta-d-galactopyranoside (1), five new flavonoids, containing the rarely isolated aglycon tamarixetin, were isolated from a methanolic extract of the endemic Balkan species Astragalus thracicus Griseb. Three of the new compounds are substituted with 3-hydroxy-3-methylglutaryl residue (HMG), untypical for the genus Astragalus. The compounds were identified as tamarixetin-3-O-alpha-l-rhamnopyranosyl-(1 -> 2)-[6-O-(3-hydroxy-3-methylglutaryl)]-beta-d-galactopyranoside (2), tamarixetin-3-O-(2,6-di-O-alpha-l-rhamnopyranosyl)-beta-d-galactopyranoside (3), tamarixetin 3-O-beta-d-apiofuranosyl-(1 -> 2)-beta-d-galactopyranoside (4), tamarixetin-3-O-beta-d-apiofuranosyl-(1 -> 2)-[6-O-(3-hydroxy-3-methylglutaryl)]-beta-d-galactopyranoside (5), and tamarixetin-3-O-beta-d-apiofuranosyl-(1 -> 2)-[alpha-l-rhamnopyranosyl-(1 -> 6)]-beta-d-galactopyranoside (6). Selected compounds from A. thracicus were tested to evaluate their anticollagenase activity. The greatest effect was observed for quercetin-3-O-beta-d-apiofuranosyl-(1 -> 2)-beta-d-galactopyranoside, possibly due to the presence of an ortho-dihydroxy arrangement of flavonoid ring B. The effect on collagenase and elastase was further evaluated also by in silico study, and the test compounds showed some level of in silico interaction.