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Abstract 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 conservedLARMcis-regulatory hub. However,lmx1bbexpression in median fins is unaffected by removal of theLARM, suggesting its regulation is an evolutionary innovation specific to the paired appendages. Although we find theLARMis highly conserved across gnathostomes, we identify specific alteration of this region in hillstream loaches, fishes which naturally parallel “double-ventral” fin phenotypes observed inlmx1bbandLARMmutants. Altogether our findings indicateLARM-mediated dorsal identity is an ancestral feature of paired appendages that provide a prepattern for limb evolution and lineage diversification.