Summary Upon nitrogen starvation, filamentous cyanobacteria develop heterocysts, specialized cells devoted to the fixation of atmospheric nitrogen. Differentiation of heterocyst at semi‐regular intervals along the filaments requires complex structural and functional changes that are under the control of the master transcriptional regulator HetR. NsiR1 (nitrogen stress‐induced RNA 1) is a HetR‐dependent non‐coding RNA that is expressed specifically in heterocysts from a very early stage of differentiation. In the genome of Nostoc sp. PCC 7120 there are 12 tandem copies of nsiR1 (nsiR1.1 to nsiR1.12), seven of them with identical sequence (nsiR1.3 to nsiR1.9) and the others slightly divergent. nsiR1.1 is transcribed antisense to the 5′ UTR of hetF, a gene required for heterocyst development. Here, we show that binding of NsiR1.1 inhibits translation of the hetF mRNA by inducing structural changes in its 5′ UTR. Altered levels of NsiR1 result in different phenotypic alterations including enlarged cell size and delayed heterocyst development that could be related to a reduced amount of HetF.