RNA extraction from mangrove tissues can be difficult due to the presence of polyphenolic and polysaccharide compounds upon cell disruption. Besides, a successful RNA isolation from mangrove tissues sometimes can be strain and species specific. Two different methods were used to extract RNA from tissues (stems, leaves and roots) of black mangrove (Avicennia germinans) and white mangrove (Laguncularia racemosa), collected from the mangrove area at Progreso, Yucatan, Mexico. An optimized and modified total RNA isolation method was developed for these recalcitrant species. The protocol is based on the CTAB method including β-mercaptoethanol and PVPP with sequential Phenol/Chloroform/isoamyl alcohol extractions to remove protein, and polyphenols, followed by two selective purifications with LiCl and sodium acetate to eliminate polysaccharides. Although, the introduced modifications are not new, their addition proved to be decisive for success in RNA isolation. This modified procedure resulted in high quantity and quality RNA. The RNA obtained is suitable for cDNA synthesis, RT-PCR experiments and the phytochelatin synthase 1 gene amplification.