MLO is a unique gene family which is identified in plant and carries out abiotic and biotic stress responses in various plants. The understanding on the roles and functional diversity of this family is quite limited in rice, a model crop plant. Rice genome has 12 potential MLO family members. To do systematic functional assignment of MLO family in rice, we performed phylogenomic analysis of integrating meta-expression data based on public sources of microarray data or RT-PCR data into the phylogenic tree. As a result, we identified 12 MLO genes carrying various tissue-preferred expression patterns such as leaf, root, pollen, and ubiquitous expression, suggesting functional diversity in terms of anatomy or development. RT-PCR analysis confirmed, integrated transcriptome data were used to estimate the functional redundancy or specificity among MLO family: MLO12 showed mature pollen preferred expression; MLO4, root tip; MLO10, overall root except root tip; MLO8, leaf; MLO2 and MLO9 showed redundant expression in overall tissues except root. Also, abiotic stress meta-expression data and RT-PCR performance suggested the functional association of 5 MLO and 6 MLO genes with heat and cold stress, respectively. Our analysis will provide basic information to study diverse developmental or physiological phenomena mediated by MLO family in rice, a major model crop plant.