ADP-ribose-1′′-monophosphatase containing A1pp or MACRO domain is an important processing enzyme in cells, participating in splicing the t-RNA procedures and catalyzing ADP-ribose-1′′- monophosphate into ADP-ribose. We identified two genes, AT1G69340 and AT2G40600, in Arabidopsis thaliana and found that, although there were many differences in amino acid, the spatial structure of conserved region was similar. We also analyzed the difference in sequence of promoter, coding region and untranslated region using the data from the whole genome of 19 ecotypes and compared both genes’ expression in different tissues in Col-0 and in seedlings in 19 ecotypes based on AtGenExpress database and the RNA-seq data, respectively. We found the same gene had different expression patterns in some ecotypes and the two genes had the similar expression patterns except in floral organs and seeds according to the data of Col-0. These results implied that the regulatory mechanisms of these genes’ expressions had changed in these ecotypes for the diversities of transcription factors and transcription factor binding sites. Above all, our research will provide some information for description of the gene function and the ecotype candidates used to study the genes’ function.