Molecular tools adapted from Transcriptionally Activator-Like Effectors (TALEs) and the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR) loci that confer adaptive immunity in bacteria and archaea have applied for genome engineering in eukaryotes. We have used these tools to induce targeted mutagenesis at endogenous loci in several plant species. However, the efficiency of editing varies between species and between targets, mutations are often observed at non-target loci, and the use of wild-type Cas9 limits engineering to target loci containing a canonical NGG motif. We are developing an expanded toolbox of molecular tools for RNA-guided Cas-mediated plant genome engineering to improve specificity and to increase the number of available of potential target sites in plant genomes. We are also developing molecular tools for the rapid, inducible activation and repression of endogenous genes, to allow refined and temporal investigations of specific gene regulatory sequences.