We used proteomic profiling to taxonomically classify extinct, alongside extant bird species using mass spectrometry on ancient bone-derived collagen chains COL1A1 and COL1A2. Proteins of Holocene and Late Pleistocene-aged bones from dodo (Raphus cucullatus) and great auk (Pinguinus impennis), as well as bones from chicken (Gallus gallus), rock dove (Columba livia), zebra finch (Taeniopygia guttata) and peregrine falcon (Falco peregrinus), of various ages ranging from the present to 1455 years old were analysed. HCl and guandine-HCL-based protein extractions from fresh bone materials yielded up to 60% coverage of collagens COL1A1 and COL1A2, and extractions from ancient materials yielded up to 46% coverage of collagens COL1A1 and COL1A2. Data were retrieved from multiple peptide sequences obtained from different specimens and multiple extractions. Upon alignment, and in line with the latest evolutionary insights, protein data obtained from great auk grouped with data from a recently sequenced razorbill (Alca torda) genome. Similarly, protein data obtained from bones of dodo and modern rock dove grouped in a single clade. Lastly, protein data obtained from chicken bones, both from ancient and fresh materials, grouped as a separate, basal clade. Our proteomic analyses enabled taxonomic classification of all ancient bones, thereby complementing phylogenetics based on DNA.