Protein HU was purified from the cyanobacterium Anabaena 7120. Its complete amino acid sequence was determined by automated Edman degradation of the whole protein and of CNBr and chymotryptic peptides. The active DNA-binding protein is a homodimer of 94-amino acid subunits. Approximately half of the residues are identical to those of the two subunits of HU protein from E. coli. The protein binds to both supercoiled and relaxed double-stranded DNA, cooperatively. The contour lengths of circular DNAs were reduced up to six-fold by HU binding at low ratios of HU to DNA. At higher ratios, highly condensed aggregates were observed. Heterocysts are cells specialized for nitrogen fixation that differentiate at regular intervals along the filaments of Anabaena when they are transferred to a medium lacking combined nitrogen. Protein HU, labeled with 35S in cells growing on ammonia, disappears from developing heterocysts, although it is stably maintained in the intervening strings of vegetative cells. Following establishment of the heterocyst pattern, in which the differentiated cells are spaced about ten cells apart, HU is synthesized in the vegetative cells but not in the heterocysts. Several other vegetative cell DNA-binding proteins are also degraded during the differentiation. The major DNA-binding protein in heterocysts is a new one of subunit molecular mass around 12,000, whose relationship to other DNA-binding proteins is unknown. The gene encoding protein HU was cloned from Anabaena DNA and sequenced. The gene sequence is consistent with the amino acid sequence determined previously. Low stringency hybridization to Anabaena DNA digests suggest that there is a single gene for HU, consistent also with the unique amino acid sequence. S1 nuclease protection experiments suggest that the HU gene promoter differs from those of other Anabaena genes determined to date.