Limb function requires polarized anatomy across the dorsal-ventral (DV) axis, but it is unclear when the capacity for DV differentiation of paired appendages arose in evolution. Here we define ancestral DV patterning programs in the fins of fishes. We show that the orthologue of the limb dorsal determinant, Lmx1b, is required to establish dorsality in zebrafish pectoral fins and is regulated by a conserved cis-regulatory hub. However, expression in median fins is unaffected by removal of the , suggesting its regulation is an evolutionary innovation specific to the paired appendages. Although we find the is highly conserved across gnathostomes, we identify specific alteration of this region in hillstream loaches, fishes which naturally parallel "double-ventral" fin phenotypes observed in and mutants. Altogether our findings indicate -mediated dorsal identity is an ancestral feature of paired appendages that provide a prepattern for limb evolution and lineage diversification.