Good quality RNA is essential for a range of analyses including microarray and gene expression studies. A number of methods for RNA extraction from symbiotic dinoflagellates were assessed for their ability to recover a high-quality RNA applicable for evaluation of gene expression profiles. The recovery and quality of the obtained RNA were evaluated with respect to UV light absorbance profiles and automated microcapillary electrophoretic RNA separation. A modified RNA extraction procedure that combines two existing commercial kits, Trizol and Qiagen RNeasy kits, was efficiently employed for the recovery of a high-quality RNA under specific homogenization conditions. Cell homogenization using glass beads at the speed of 4,500 rpm for up to 6 min resulted in a good RNA recovery and preserved RNA integrity. A high-quality RNA obtained following the described procedure was successfully applied in reverse transcriptase-polymerase chain reaction (PCR) and in quantitative PCR studies. Gene expression profiles were changed with RNA extraction procedure, with the highest transcript numbers at precise conditions of cell homogenization. RNA samples with RNA integrity number values from 6 and above were recommended for downstream applications. This sequence of RNA isolation and RNA evaluation represents a methodological improvement required for functional genomic studies in dinoflagellates.