•Type III systems were the first to provide key aspects of the molecular mechanisms underlying CRISPR-Cas immunity.•Immunity only occurs if the target is transcribed.•The underlying molecular mechanism requires co-transcriptional cleavage of the target DNA and its transcripts.•Mobile genetic elements that silence their genomes are tolerated by Type III CRISPR-Cas immunity. Type III CRISPR-Cas systems have a unique targeting mechanism that requires the transcription of the DNA target and results in the degradation of not only the genome of the invader but also its transcripts. Here we discuss the most recent studies describing dual DNA and RNA targeting by these systems, as well as the implications of this complex molecular mechanism for immunity in vivo.