For the Cuban littorals in the Caribbean Sea, information on benthic diatoms is scarce, and hitherto non-existent for natural protected areas. Thus, to describe the structure of benthic diatom associations (BDAs) from a marine protected area in Cuba, sediment samples were collected in Playa Las Gaviotas (Refugio de Vida Silvestre Cayo Santa María) during dry (November) and rainy (July) seasons. Diatoms were separated, mounted in synthetic resin and identified under light microscopy. Species diversity of the BDA was estimated using Shannon (H′), Simpson (1 − λ) and Pielou evenness (J′) indices. We identified 354 taxa including 200 new records for Cuba; the nomenclature of 45 previously recorded taxa was updated. The currently recorded species richness of marine benthic diatoms for Cuba is 595. The most abundant taxa were Amphora cf. copulata, A. proteus, Diploneis smith var. pumila, Halamphora turgida, H. coffeiformis, Navicula zostereti, Nitzschia marginulata var. didyma and Psammodictyon panduriforme. The best-represented genus was Mastogloia with 70 taxa. Similarity values indicated homogeneous distribution of epipelic diatom taxa along the sandy bottom, suggesting a single diatom association. Mean values of H′ ranged from 4.91 bit/taxon in November to 4.95 bit/taxon in July. Structure analysis suggests a stable BDA with high species diversity characteristic of productive, pristine environments.

During a floristic inspection of sediment samples from Playa Las Gaviotas, 69 specific and infra-specific taxa of Mastogloia were identified in the diatom taxocenosis, including 42 unrecorded taxa for the Cuban coasts. These are added to the 59 Mastogloia taxa previously listed. In this way, currently, the 101 Mastogloia comprised in the benthic diatom associations of the Cuban coast constitute the highest number of taxa ever recorded in similar floristic studies, which also indicates their tropical affinity. Furthermore, observations are made on misidentified taxa such as Mastogloia (Orthoneis) aspera, M. asperuloides, M. (Orthoneis) clevei, M. floridensis, M. latecostata, M. laterorostrata, M. ovata, M. sigillata, M. pseudolatecostata, and others.