AbstractHigh quality RNA is a crucial requirement in a variety of analyses including next generation sequencing, microarray, and gene expression studies. A number of protocols for the extraction of ribonucleic acids from algae are currently in use, but different reagents interfere with buffer capacities and therefore lower the success of the isolations. The diversity of microalgae is reflected in a large variety of biomolecules and so far no standard protocol for the extraction of RNA from these highly divergent groups has been assessed. With this study, 11 conventional protocols are compared and an alternative standardized protocol for the isolation of high quality total RNA is proposed. Furthermore, the extraction method is applied on four different microalgae species of the Chlorophyta, Charophyta, Rhodophyta, and a dinoflagellate. We present an optimized RNA extraction method, yielding total RNA of high purity and integrity from all the investigated protists. The protocol provided in this study is cost‐effective and can assist in future functional genomics, covering an essential step when working with RNA from non‐model microorganisms.