The filamentous heterocyst‐forming cyanobacterium Anabaena sp. PCC 7120 is an important model organism for studying cell differentiation, nitrogen fixation, and photosynthesis. This cyanobacterium possesses a high number of membrane transporters. Not much is known about the roles of the membrane transporters, especially the ATP‐binding cassette (ABC) transporters, in the multidrug resistance of this cyanobacterium. In the present work, we performed a mutational analysis of the genes alr4280/alr4281/alr4282 and alr3647/alr3648/alr3649 that code for the components of putative ABC exporters and are homologous to the DevBCA heterocyst‐specific glycolipid exporter. We show that these genes are essential for resistance to different drugs and are not essential for heterocyst development.