A filamentous benthic cyanobacteria strain isolated from a tropical man-made pond in Malaysia was characterised using combined phenotypic and genetic approaches. Morphological and ultrastructural observations were performed together with growth measurements. Cell dimensions, thylakoid arrangement and apical cell shape with aerotopes were consistent with the description of Pseudanabaena amphigranulata (Goor) Anagnostidis. Molecular characterisation of the16S rRNA gene gave 94% pairwise sequence identity with Pseudanabaena sp. PCC 6802,which corresponds to the genus identification threshold value while also suggesting that the strain is distinctly different to the species of Pseudanabaena currently represented in available databases. The strain showed identical 16S-23S ITS configuration with other strains of Pseudanabaena apart from having a larger spacer region. Cultures of the strain were exposed to various temperature and photoperiod treatments and harvested at exponential phase in order to examine phenotypic plasticity. Significant relationships between environmental conditions and morphological characteristics (cell dimensions and shape) were identified for the first time within the genus Pseudanabaena. The maximum cell length (5.7 ± 0.07 μm) was observed at 25 °C under 12:12 light to dark, while the greatest cell width (3.2 ± 0.11 μm) was also observed at 25 °C but under 16:8 light to dark. The strain showed high plasticity in cell dimensions and shape under different temperature and photoperiod treatments, with25 °C under 12:12 light to dark providing the optimal conditions for its growth.