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Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single‐locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partialcox1,rbcL,5.8S + ITS2,ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species ofEunotia,Seminavis, Nitzschia, SellaphoraandPseudo‐nitzschiacorresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.

“Surf diatoms” can form high biomass in the surf zone of sandy beaches around the world,AsterionellopsisandAnaulusbeing the main genera of this group in Brazil.Asterionellopsis glacialiswas considered a cosmopolitan species, and taxonomic studies using molecular and morphological tools showed thatA. glacialisis a complex with cryptic and semicryptic species. So, it would be plausible to suppose thatAnaulus australis, another surf zone patch-forming diatom with wide latitudinal occurrence could also be part of a species complex. We collected and identifiedAnaulusandAsterionellopsisstrains from tropical, subtropical and warm temperate sandy beaches on the east coast of South America (Brazil) based on genetic divergence, phylogeny, single-locus automated species delimitation methods (both genera), and frustule ultrastructure (Anaulus).AnaulusandAsterionellopsisshowed contrasting diversity patterns and spatial distribution: a single species ofAnaulus australiswas registered in tropical and subtropical beaches, while at least three species ofAsterionellopsis:A. tropicalis,A. thurstoniiandA. guyunusaewere observed at different latitudes, indicating thatAsterionellopsisspecies have distinct ecological requirements.Asterionellopsis thurstoniiwas previously reported in Europe and it is documented here for the first time in the Southern Hemisphere. The different diversity patterns between these two surf diatom genera suggest that they are likely to have distinct ages, and dispersion and/or speciation processes.