Rhipicephalus microplus is one of the most widely distributed and economically important ticks able to transmit pathogens to vertebrate hosts which cause major constraints to public and livestock health. A better understanding of their population structure is crucial for the development of more effective control strategies. Modern morphometrics has enabled the quantification of size and shape variations to investigate population differences in anatomical structures. We therefore applied landmark-based and outline-based geometric morphometric approaches to study 85 field-collected adult females of three R. microplus Colombian populations along a distance of 28–67 km using the scutum and the basis capituli. Although size differences were found between some populations, mean shape and metric disparity of the analyzed structures were very similar, resulting in low classification scores (<41%). Thus, both structures support a metapopulation of R. microplus at a microgeographic level. The variance of shape between structures does not co-vary, likely indicating morphological modularity. These data provide first clues to understand the metric variation of R. microplus among natural populations from north-western Colombia.