Engineered TALENs (Transcription activator-like effector nucleases) and CRISPR/Cas (clustered regularly interspaced short palindromic repeats/ CRISPR-associated proteins) as genetic toolbox have been widely used in basic and applied biological researches. Here we use TALENs and CRISPR/Cas9 to target miRNA genes and Argonaute (AGO) genes for gene knockouts and study their functions in rice. We successfully knocked out 5 miRNA genes and recovered phenotypic mutant plants using TALENs. The efficient assembling of TALENs constructs and their versatility provided us a very useful toolbox to study miRNA gene functions. In addition, we used CRISPR/Cas9 system to target AGO genes in rice. We successfully generated single-gene knockouts for all 19 AGO genes and several multi-gene mutants of gene clades through multiplex targeting of CRISPR system in rice. Some mutants were characterized at molecular and morphological levels. The results demonstrate TALEN and CRISPR/Cas9 mediated gene editing are robust genetic tools that enable functional genomics.