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Long noncoding RNAs (lncRNAs) are known to play important roles in several plant processes such as flowering, organ development and stress response. However, studies exploring the diversity and complexity of lncRNAs and their mechanism of action in plants are far fewer that those in animals. Here, we show that an intronic lncRNA in rice (Oryza sativa L.), RICE FLOWERING ASSOCIATED (RIFLA), is required for the inhibition of OsMADS56 expression. RIFLA is produced from the first intron of the OsMADS56 gene. Overexpression of RIFLA in rice repressed OsMADS56 expression but activated the expression of flowering inducers Hd3a and RFT1. Additionally, RIFLA -overexpressing transgenic rice plants flowered earlier than the wild type. Under normal conditions, the transcript level of the rice enhancer of zeste gene OsiEZ1 , a homolog of Arabidopsis histone H3K27-specific methyltransferase genes SWINGER (SWN) and CURLY LEAF (CLF), was as low as that of RIFLA , whereas the transcript level of OsMADS56 was relatively high. In the osiez1 mutant, OsMADS56 expression was upregulated, whereas RIFLA expression was downregulated. Additionally, RIFLA formed a complex with OsiEZ1. Together, these results suggest that the floral repressor activity of OsMADS56 is epigenetically regulated by RIFLA and OsiEZ1. • Intronic lncRNA RIFLA is produced from the first intron of the OsMADS56 gene. • RIFLA directly interacts with histone methyltransferase OsiEZ1. • OsMADS56 expression is upregulated in RIFLA -overexpressing plants. • Overexpression of RIFLA in rice causes early flowering. [ABSTRACT FROM AUTHOR]