The development of molecular tools that enable precise manipulation and control of biological systems would allow for a broader understanding of cellular functions and applications in biotechnology, synthetic biology, and therapeutic research. The discovery of CRISPR/Cas systems and the understanding and repurposing of their mechanisms have revolutionized the field of molecular biology. Here, I identified and characterized novel CRISPR/Cas systems and applied them for different in vivo and in vitro applications. In this work, I interrogated various Cas13 effector proteins and identified the most efficient Cas13 effector (CasRx) for in planta applications. I adapted CasRx to engineer plant immunity against different plant RNA viruses. CasRx showed robust activity and specificity against RNA viruses, demonstrating its suitability for studying key questions relating to virus biology. To expand the Cas13 toolbox and enable new applications, I performed a homology search of Cas13 enzymes in prokaryotic genomes and metagenomes, and identified previously uncharacterized, novel CRISPR/Cas13 effector proteins. I first identified and functionally characterized a small size, miniature Cas13 effector (named here as mCas13) and combined it with isothermal amplification to develop a simple and sensitive CRISPR-based SARS-CoV-2 diagnostic platform. In addition, I discovered and biochemically characterized the first known thermostable Cas13 proteins and showed that these thermostable proteins are phylogenetically related. I harnessed the unique features of these thermostable enzymes to develop the first one-pot, RT-LAMP coupled Cas13-based nucleic acid detection assay, which was utilized for highly sensitive, specific, and easily programmable detection of SARS-CoV-2 and other viruses. Lastly, I utilized CRISPR/Cas12a to develop a detection assay of plant ssDNA geminiviruses with easy-to-interpret visual readouts, making it suitable for point-of-use applications. In addition, I leveraged the self vs. non-self-discrimination and pre-crRNA processing capabilities of CRISPR/Cas12a, with the allosteric transcription factors (aTFs)- regulated expression of CRISPR array to engineer a field-deployable small molecule detection platform. I demonstrated the ability of the developed platform to detect different tetracycline antibiotics with high sensitivity and specificity. In conclusion, my work demonstrates that the discovery and characterization of programmable nucleic acid targeting systems could enable their utility for biotechnological innovations, including technologies for inhibition of viral replication and diagnostics.