ATP-binding cassette transporters (ABCT) could generate multiple transcripts through alternative splicing (AS) in mammalian. Some AS introduced PTC (premature terminal codon)-containing isoforms of ABCT couple with NMD (nonsense-mediated mRNA decay) to regulate relevant functions. However, there are no similar reports in lower organisms. This paper focuses on the unicellular protozoa Tetrahymena thermophila, based on the RNA-seq data of Tetrahymena thermophila, identified two alternative splicing variants of gene ABCC10 (SV1 and SV2). The SV2 contained an intron retention event at the fifth intron, and this 49 bp intron resulted in shift-frame and introduced PTC. Then, a knock-down Tetrahymena strain of gene UPF1 which is a key factor of NMD was constructed, and the expression levels of SV2 were performed using a real-time quantitative PCR. The results showed the expression levels of SV2 were up-regulated significantly in knock-down strain, indicating that SV2 was targeted by NMD, which is consistent to the mechanism which the AS introduced PTC-containing isoforms of ABCC proteins can be targeted by NMD in mammalian. Thus, we infer that this mechanism is highly evolutionary conserved in eukaryotes and was already functional in the last eukaryotic common ancestor.