Plants are highly sensitive to temperature changes and several mechanisms operate at the levels of photoreceptors to nucleosomes to confer thermal responses in plants. High ambient temperatures induce flowering in Arabidopsis and it has been proposed that alternative splicing of FLOWERING LOCUS M (FLM) that results in transcripts with antagonistic effects mediate this response. We present an alternative model and show that elevated temperatures affect splicing of FLM to induce several splice variants that are targeted by the nonsense-mediated mRNA pathway (NMD) that leads to a reduction in the FLM expression levels.  Our findings suggest a novel pathway in which derepression of floral inhibition is achieved through a degradation of the repressors either at the RNA level or at the protein level. We also present a novel method to quantify splicing efficiencies and using this novel tool demonstrate a method to identify splice sites that are affected by environment, development or genetic variation.