Several cyanobacteria, including diazotrophic Raphidiopsis raciborskii, can form harmful blooms when dissolved inorganic phosphorus (DIP) concentrations are very low. We hypothesized that R. raciborskii strains would vary in P allocations to cell growth and storage, providing resilience of populations to continuously low or variable P supplies. We tested this hypothesis using six toxic strains (producing cylindrospermopsins) isolated from a field population using batch monocultures with and without P and dissolved inorganic nitrogen (DIN). Treatments replete with DIN, irrespective of P addition, had similar exponential growth rates for individual strains. P storage capacity varied four-fold among strains and was significantly higher in DIN free treatments than in replete treatments. P was stored by all R. raciborskii strains, in preference to allocation to increase growth rates. P stores decreased with increased growth rate across strains but were not related to the time to P starvation in P free treatments. The storage capacity of R. raciborskii, combined with strategies to efficiently uptake P, mean that P controls may not control R. raciborskii populations in the short-term. Intra-population strain variation in P storage capacity will need to be reflected in process-based models to predict blooms of R. raciborskii and other cyanobacteria adapted to low-P conditions.