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Abstract Long non-coding RNAs (lncRNAs) are abundant in plants, however, their regulatory roles remain unclear in most biological processes, such as response in salinity stress which is harm to plant production. Here we show a lncRNA inMedicago truncatulaidentified from salt-treated Medicagotruncatulais important for salinity tolerance. We name the lncRNALAL,LncRNAANTISENSEtoM. truncatulaLIGHT-HARVESTING CHLOROPHYLL A/B BINDING(MtLHCB)genes. LALis an antisense to four consecutiveMtLHCBgenes on chromosome 6. In salt-treatedM. truncatula,LALis suppressed in an early stage but induced later; this pattern is opposite to that of the fourMtLHCBs. Thelalmutants show enhanced salinity tolerance, while overexpressingLALdisrupts this superior tolerance in thelalbackground, which indicates its regulatory role in salinity response. The regulatory role ofLALonMtLHCB1.4is further verified by transient co-expression ofLALandMtLHCB1.4-GFPin tobacco leaves, in which the cleavage ofMtLHCB1.4and production of secondary interfering RNA is identified. This work demonstrates a lncRNA,LAL, functioning as a regulator that fine-tunes salinity tolerance via regulatingMtLHCB1s’ expression inM. truncatula.