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Selecting native species for ecological restoration remains a challenge, especially when the commercial supply of seedlings does not adequately represent the regional flora. We used the tree flora of Iguaçu National Park as a regional ecological reference to assess its similarity to the species available in forest nurseries in the surrounding region and propose a multicriteria protocol. We sampled 471 individuals belonging to 73 species and 30 botanical families in six permanent plots in Iguaçu National Park. Similarity between the local flora and the nurseries was low, ranging from 0.11 to 0.16, whereas similarity among nurseries was moderate, ranging from 0.438 to 0.574, indicating that seedling supply is partially homogeneous and poorly representative of the reference flora. Based on these results, we applied a weighted multicriteria protocol integrating ecological, operational, and normative criteria to prioritize native species for seedling production in regional nurseries. Phenology, seed storage behavior, threat status, and dormancy were identified as the attributes with the greatest relative contribution to category differentiation. The protocol provides a technical and scientific basis to guide nurseries and restoration actions based on the local reference flora.