Although diverse natural products have been isolated from the benthic, filamentous cyanobacterium Lyngbya majuscula, it is unclear whether this chemical variation can be used to establish taxonomic relationships among disparate collections. We compared morphological characteristics, secondary-metabolite compositions, and partial 16S ribosomal DNA (rDNA) sequences among several collections of L. majuscula Gomont, Lyngbya spp., and Symploca spp. from Guam and the Republic of Palau. The morphological characteristics examined were cell length, cell width, and the presence or absence of a calyptra. Secondary metabolites were analyzed by twodimensional thin-layer chromatography. Each collection possessed a distinct cellular morphology that readily distinguished Lyngbya spp. from Symploca spp. Each collection yielded a unique chemotype, but common chemical characteristics were shared among four collections of L. majuscula. A phylogeny based on secondarymetabolite composition supported the reciprocal monophyly of Lyngbya and Symploca but yielded a basal polytomy for Lyngbya. Pairwise sequence divergence among species ranged from 10 to 14% across 605 bp of 16S rDNA, while collections of L. majuscula showed 0 to 1.3% divergence. Although the phylogeny of 16S rDNA sequences strongly supported the reciprocal monophyly of Lyngbya and Symploca as well as the monophyly of Lyngbya bouillonii and L. majuscula, genetic divergence was not correlated with chemical and morphological differences. These data suggest that 16S rDNA sequence analyses do not predict chemical variability among Lyngbya species. Other mechanisms, including higher rates of evolution for biosynthetic genes, horizontal gene transfer, and interactions between different genotypes and environmental conditions, may play important roles in generating qualitative and quantitative chemical variation within and among Lyngbya species.The benthic, filamentous cyanobacterium Lyngbya majuscula Gomont is distributed throughout the tropics in reef and lagoonal habitats (18,61,62), often forming dense mats that carpet benthic substrates. L. majuscula can compete with macroalgae (59) and is unpalatable to fish, crabs, urchins, and other macroherbivores (43,50,57). However, specialized mesoherbivores, such as the sea hare Stylocheilus striatus, may preferentially consume L. majuscula (8,41,51). Secondary metabolites produced by L. majuscula are responsible for both the deterrence of feeding by macroherbivores and the stimulation of feeding by mesoherbivores (41,51,57).Over 100 novel secondary metabolites have been isolated from collections of L. majuscula. Although these collections have been globally distributed, there is little evidence that any given types of secondary metabolites are associated with specific geographic regions (10). Indeed, collections within limited geographic areas are often extremely diverse. On Guam, L. majuscula collections have yielded indanone metabolites (45), lyngbyastatins (16,27,64), malyngamides (4, 5, 38), malyngolide (7), majusculamides (35), ...