<p>This study investigates the variability in morphometric (body size and pelage colour) traits to establish discriminant criteria for accurately identifying syntopic <i>Apodemus</i> species in NE Spain. Despite genetic divergence, in SW Europe these cryptic species present challenges in field identification due to their morphological similarities. Sampling campaigns were conducted in deciduous forests from Navarra and Barcelona, employing live-trapping methodologies, and individuals captured were accessioned as voucher specimens for biometric and colorimetric analyses. We found significant morphological and colorimetric differences between <i>A. flavicollis</i> and <i>A. sylvaticus</i>, namely large size and high pelage contrast in the former (higher lightness and chroma). Our results suggested that ventral colour variability was higher than dorsal, and ventral colour variables had stronger discriminating power among species. Indeed, a discriminant function, combining ventral colour and body size, allowed correct classification of 96.4% of the individuals among species. The dorsal coloration of both species was similar, suggesting convergent evolution driven by crypsis. Despite being the base of ecological studies on coat coloration (e.g., Gloger’s rule), dorsal colour was less useful for differentiating species. Analysis of ventral coloration for species identification was normally dismissed by investigators, and we propose the need of potentially including ventral colour assessment when working with cryptic species. Our approach, using museum skins and a flatbed scanner with standardized illumination, yielded more precise coat colour data than internet images, allowing for detection of subtle chromatic variations. The integrated approach, combining biometric and colorimetric data, provided a robust framework for understanding the phenotypic variability and potential ecological adaptations of these closely related rodents.</p>