RNA editing involves the post-transcriptional modification of genes, whereas alternative splicing involves both post- and co-transcriptional regulation of gene expression. Our previous findings reported that tissue and different developmental stage-specific alternative splicing and RNA editing occur in pentatricopeptide repeat (PPR) family genes. In this study, we found that important Zinc Finger (ZnF) genes undergo tissue-specific alternative splicing, which affects protein structure and function. Five ZnF genesthat were likely to undergo alternative splicing were selected based on their functional importance. Most of these genes are located in protein-coding regions, which were predicted using the Arabidopsis database. Tissue-specific alternative splicing in all five ZnF genes was confirmed by quantitative PCR and sequencing. AT1G75340/ZnF2c, AT1G75340/ZnF2d, AT3G61850/ZnF3b, AT1G06040/ZnF5b show intron retention, AT2G47850/ZnF1b contains a 3'alternative splice site, and exon skipping is detected in AT1G75340/ ZnF2a. Alternative splicing events occurred in the coding regions of four genes and in the 3' UTR of AT3G51950/ ZnF4. We identified three novel and previously unannotated alternatively spliced isoforms by quantitative PCR analysis and sequencing; ZnF4b arose from an alternative 3' splice site and ZnF2c, ZnF2d from intron retention. AT2G47850/ ZnF1 and AT3G61850/ZnF3 isoforms affect protein structures, ligand binding sites and ultimately functions. There were previously unannotated isoforms AT1G75340/ZnF2c and AT1G75340/ZnF2d that resulted in frameshift mutations. The functionality of alternatively spliced isoforms need to be elicited in plant physiology.