Commensal rodents are a very important group of animals because of their close affinity to humans. Understanding their diversity in the archaeological context is crucial for reconstructing the anthropization process of past environments. Two important archaeological sites in the Philippines were chosen for this study because of their well-established chronology; Callao Cave in Cagayan Valley and Ille Cave in Palawan. Furthermore, both the locations of these caves are characterized by distinct biogeography. We aim to describe the diversity of commensal rodents from these sites to detect change in rodent communities over time that potentially infers local environmental change. Here, we use geometric morphometrics (GMM) on the first lower molars and mitochondrial cytochrome b analysis on archaeological, museum, and modern specimen from these archaeological sites and adjacent regions in the Philippines. We find that there are distinct molar morphologies in the dataset. The Principal Component Analysis results show that using both size and shape increases the degree of confidence in separating species. Landmark-based and outline analysis approaches could also be used in tandem for more refined results in species identification using GMM. We also find that there is genetic diversity previously uncharacterized in the region. Lastly, when supplemented by archaeozoological analysis, the approaches serve as an effective tool for investigating shifts in rodent taxa representation in the chronology of the sites. Our findings demonstrate the potential of using the combination of archaeozoological, dental morphological analysis, and genetic analysis on commensal rodents to infer for past environmental changes.