Controlled proteolytic activation of membrane-bound transcription factors (MTFs) is recently emerging as a versatile way of rapid transcriptional responses to environmental changes in plants. Here, we report genome-scale identification of putative MTFs in the Arabidopsis and rice genomes. The Arabidopsis and rice genomes have at least 85 and 45 MTFs, respectively, in virtually all major transcription factor families. Of particular interest is the NAC MTFs (designated NTLs): there are at least 18 NTLs in Arabidopsis and 5 NTL members (OsNTLs) in rice. While the full-size OsNTL forms are associated with the membranes, truncated forms lacking the transmembrane domains are detected exclusively in the nucleus. Furthermore, transcript levels of the OsNTL genes were elevated after treatments with abiotic stresses, supporting their roles in plant stress responses. We propose that membrane-mediated transcriptional control is a critical component of gene regulatory network that serves as an adaptive strategy under unfavorable growth conditions.