Methyl chloride and methyl bromide, which contribute to the destruction of the stratospheric ozone layer, are mainly emitted from natural sources. It was recently reported that tropical and subtropical plants were the largest sources of methyl chloride. Furthermore, the involvement of the gene HARMLESS TO OZONE LAYER (HOL) in methyl halide emissions from Arabidopsis thaliana was demonstrated. However, neither the physiological significance of the methyl chloride emission nor the biochemical properties of HOL, denoted as AtHOL1 in our study, have been reported yet. We identified two additional isoforms-AtHOL2 and AtHOL3-from Arabidopsis and characterized them together with AtHOL1. AtHOL1 was ubiquitously expressed during development, and its expression level was the highest among the three. The phylogenetic tree suggested that AtHOL1 homologous proteins were distributed throughout the plant kingdom. Biochemical analyses showed that the three recombinant AtHOL proteins were functional and had distinct levels of the S-adenosyl-L-methionine-dependent methyltransferase activities. Although a study of AtHOL1-disrupted mutants had shown that AtHOL1 primarily controlled the production of methyl halide, our study suggested that the activation of AtHOL2 and AtHOL3 genes also contribute to the methyl halide emissions from Arabidopsis.