The global demand for the carrageenophyte Kappaphycus is steadily increasing but its overall productivity, carrageenan quality, and disease resistance are gradually declining. In the face of this dilemma, wild Kappaphycus populations and natural selective breeding are viewed as possible sources of new cultivars that could potentially enhance production and phycocolloid yield and quality. Therefore, assessment of their diversity is crucial. Morphological and genetic diversity of wild Kappaphycus species obtained from two sites in the Philippines recorded novel haplotypes along with other published haplotypes. These newly recognized haplotypes indicate a reservoir of unutilized wild genotypes in the Philippines, which could be taken advantage of in developing new cultivars with superior traits. Moreover, natural selective breeding of progenies derived from sexual and meiotic spore production can produce new generations of tetrasporophytes and gametophytes, for assessment of desirable phenotypes.