PCR and barcoding of single cells has promising applications in microalgal identification, because it provides a method for rapidly identifying species that are morphologically indistinct, unknown, or unable to be cultured. This research aims to clarify the best approach for single cell DNA amplification of vegetative and cyst-stage microalgae from seawater that is fresh, frozen, or preserved in Lugol’s solution to aid in characterising species of interest from the South Australian 2025-26 HAB event. Alternative methods to enzymatic lysis for DNA extraction from single cells were assessed, including freeze-thawing and mechanical disruption. Samples preserved in Lugol’s solution were pre-treated with sodium thiosulphate to avoid downstream impacts to PCR and sequencing. Alternative PCR conditions including modified reaction volumes and re-cycling were also investigated. The results from this research help to characterise elusive microalgae, provide positive identification references for future microscopy, and develop techniques that will allow for the utilisation of the large quantity of seawater and sediment samples that have been preserved long-term from ongoing sampling efforts undertaken by SARDI.