The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called MaskedName for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. MaskedName estimates the contributions of several source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art machine learning methods for source tracking, FEAST and mSourceTracker. We anticipate that MaskedName will be a valuable tool for MST of ancient metagenomic studies.Note: This submission is under revision in a journal at the momentSupplementary File: https://drive.google.com/file/d/1aDjWdg9Jx0f2vZqzzTC9JHcQB3Lw4IYZ/view?usp=sharing