Marine macroalgae are a prolific source of pharmacologically important secondary metabolites. However, many species used in pharmacognosy and in biomedical experiments are severely understudied biologically. Portieria, an Indo-Pacific red seaweed, is one of those understudied species found to harbor an abundance of halogenated monoterpenes. Halomon, a halogenated monoterpene with anti-tumor properties has been isolated in a Portieria population in Batanes, Philippines. Unfortunately, the absence of sufficient biological knowledge about Portieria has placed halomon in a drug development bottleneck. The motivations for this thesis are to test the hypotheses that the variation in halomon content among Portieria populations could be due to cryptic diversity, seasonality or geographical variation on the secondary metabolite production. Given these three conditions: differential production of pharmacologically important monoterpenes, lack of biological knowledge on Portieria, and the possibility of the presence of cryptic species, this thesis specifically aimed to examine cryptic diversity in Portieria; determine how this genetic diversity is expressed on the phenotypic level (morphology and chemistry) and in doing so determine the role of cryptic diversity, life-history stages, seasonality and geographical location on the differential production of secondary metabolites.