A NaCl(r) mutant of the diazotrophic cyanobacterium Anabaena variabilis has been isolated by NTG mutagenesis and selection for NaCl resistance. The NaCl(r) strain has been characterized with respect to its mechanism of NaCl tolerance and regulation of Na(+) influx. NaCl(r) strain exhibits low Na(+) influx, accumulated high level of glycine betaine as a compatible solute, and persistent synthesis of SSPs at a higher rate than its wild-type counterpart. DCMU, an inhibitor of PS-II, inhibited Na(+) influx, suggesting that Na(+) influx is an energy-dependent process and that the energy is derived from photophosphorylation. This contention is further supported by the inhibition of Na(+) influx under dark conditions. The inhibition of Na(+) influx by KCN, DNP, NaN(3) also supports the involvement of oxidative phosphorylation in the regulation of active Na(+) influx. Thus, it appears that the synthesis of SSPs, accumulation of compatible solutes, and exhibition of low Na(+) influx in the NaCl(r) strain made this organism NaCl tolerant.