<p>The analysis of morphology and body asymmetry in organisms can reveal the challenges faced during development. Populations of <i>Varroa destructor</i> exhibit morphological plasticity, but there is a lack of standardization in body structures and measurements used in research. This study aimed to identify, through geometric morphometrics, a body structure that allows for a standardized study of the morphological variations and fluctuating asymmetry of <i>V. destructor</i> in different environmental contexts. To this end, we analyzed the morphology of mites infesting colonies of Africanized honeybees in two contexts: different levels of hygienic behavior in the colonies and distinct environments (Caatinga and Atlantic Forest). Asymmetry is specifically assessed in the context of these environments. In colonies with differentiated hygienic behaviors, the metapodal shield showed a higher classification rate between groups (70%) than the genitoventral shield (64%), and it was the only structure that showed significant size differences between groups (<i>p</i> &lt; 0.001). In mites from different geographic regions, the metapodal shield also exhibited a higher classification rate (78%) than the genitoventral shield (65%), with no significant difference in the size of the shields between the mite populations. Significant differences in fluctuating asymmetry were observed in the shape and size (<i>p</i> &lt; 0.001) of the pair of metapodal shields and the shape of the genitoventral shield (<i>p</i> &lt; 0.001). The results provide important methodological and ecological insights, highlighting the metapodal shield as a reliable structure for assessing shape, size, and fluctuating asymmetry. This standardization can improve consistency across studies and parasite monitoring.</p>