CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems arose in bacteria and archaea as adaptive immune systems to combat foreign genetic elements. Cas13 (formerly C2c2) is an RNA-guided nuclease that base-pairs with complementary RNA to activate its higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains. Once activated, the HEPN domains will cleave bound target-RNA in cis and off-target single-stranded RNA in trans. Target-RNA dependent trans-cleavage by Cas13 has been harnessed to detect RNA in complex mixtures while cis-cleavage has been leveraged as a tool for specific RNA targeting in mammalian, plant, and yeast cells. Remarkably, the family of Cas13 enzymes are highly functionally and evolutionarily divergent; different orthologs target RNA with variable efficacy and diverged HEPN-nulceases show discrete RNA substrate preferences. Here, we describe our recent advances combining structural biology and high-throughput sequencing to better understand how divergent Cas13 enzymes negotiate complex RNA secondary structures, discriminate against mismatched target-RNA, and carry out catalysis.