<p>Habitat networks in planning instruments are essential for preserving biodiversity and ensuring ecological connectivity. However, varying stakeholder interpretations influence how these networks are addressed, leading to divergent spatial transpositions. This research aims to better understand how habitat networks are concretely mapped in French planning instruments. We focus on stakeholder’s practices across 21 “Schémas de Cohérence Territoriale” (SCoTs)—territorial planning instruments—in the Bourgogne Franche-Comté region. Using a mixed-methods approach, we combined textometry with qualitative analysis of 21 semi-structured interviews and the corresponding spatial mappings of habitat networks. Our findings show that habitat network representations vary considerably across planning instruments. We identified four distinct discourse categories, ranging from scientifically grounded approaches to politically negotiated strategies. The discourses also highlight methodological constraints contributing to the diversity of mapping approaches. By uncovering the link between discourse and mapping practice, this research provides insights into the challenges of integrating ecological connectivity into territorial planning.</p>