Marine cyanobacteria have emerged as a source of promising bioactive compounds. The isolation of strains from tropical environments seems to be an important step in the search for molecules displaying bioactivity, besides being valuable for biotechnological purposes. Thus, the objective of the present study was to describe marine cyanobacterial strains, isolated and characterized in terms of morphology and molecular phylogeny, as well as screened for biologically active compounds. Five strains were isolated and morphologically characterized as Leptolyngbya (CENA553, CENA554 and CENA555) and Geitlerinema (CENA552 and CENA556). Considering the phylogenetic results, these strains did not match the clusters of the type-species or reference strains, indicating the possible emergence of new generic entities morphologically related to Leptolyngbya and Geitlerinema. Among the isolated strains, CENA552 and CENA556 were selected for chemical analyses. Five known nucleosides with biological activities and two amino acids were recognized and isolated from the CENA556 strain. The GC-MS analyses of strains CENA552 and CENA556 revealed distinct classes of non-polar compounds, with a predominance of octadecane (CENA556), 2-hexyl-1-decanol (CENA552) and neophytadiene (CENA552 and CENA556) hydrocarbons. All nucleosides and amino acids were highly abundant, indicating these morphotypes as promising sources of these bioactive compounds. This is the first report considering taxonomy/molecular phylogeny as well as chemistry prospection of morphotypes resembling Geitlerinema-like isolated from the Brazilian coastal area, highlighting the potential of these taxa for biotechnological applications.