Members of MATH-BTB/POZ protein family, which participate in the ubiquitin-dependent protein degradation, affect plant response under stress conditions through the interaction with various transcription factors. Six genes (BPM1-6) in Arabidopsis thaliana L. encode for at least 16 different BPM proteins in the process of alternative gene splicing. A new research has shown an induced expression of BPM1-3 genes and a differential expression of BPM1 gene variants during plant exposure to elevated temperature. Here, effects of temperature on the expression of BPM1-3 gene variants were analyzed by using PCR method. Furthermore, the existence of new splicing variants that could be generated due to temperature variations was examined in this work. For this purpose, gene-specific primers for amplification of BPM1-3 gene variants were designed and optimized. cDNA was generated from A. thaliana seedlings which had been exposed to different temperatures and used in amplification. During this analysis, fragments which have been nonspecifically amplified, were subsequently cloned into a vector pGEM®-T Easy using TA cloning. New variant was sequenced to compare its similarity with known BPM1-3 variants. Temperature-dependent regulation of gene expression and alternative splicing of BPM1-3 genes was confirmed. A new splicing variant BPM2.6 was discovered under normal conditions and conditions of elevated temperature. Due to the absence of BTB/POZ domain which is crucial for interaction with cullin, the discovery of new splicing variant provides the basis for further research regarding cullin-independent roles of BPM proteins.