To maintain a symbiotic balance, leguminous plants have a systemic regulatory system called autoregulation of nodulation (AUT). Since AUT is schematically similar to systemic resistance found in plant-pathogen interactions, we examined the effects of methyl jasmonate (MeJA) or methyl salicylate (MeSA) on nodulation in Lotus japonicus. Shoot-applied MeJA strongly suppressed nodulation in the wild type and even hypernodulation in the har1 mutant, whereas MeSA exhibited no effect. MeJA inhibited early stages of nodulation, including infection thread formation and NIN gene expression, and also suppressed lateral root formation. These findings suggest that jasmonic acid and/or its related compounds participate in AUT signaling.