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Background and aims – The present study aims to describe a new species of pennate blue diatom from the genus Haslea, H. nusantara sp. nov., collected from Semak Daun Island, the Seribu Archipelago, in Indonesian marine waters.Methods – Assessment for species identification was conducted using light microscopy, Scanning Electron Microscopy and molecular techniques. The morphological characteristics of H. nusantara have been described, illustrated and compared to other morphologically similar blue Haslea taxa, distributed worldwide. Additionally, molecular characterization was achieved by sequencing plastidial and mitochondrial genomes.Key results – This new species, named Haslea nusantara, cannot be discriminated by its morphology (stria density) but it is characterized by its gene sequences (rbcL chloroplast gene and cox1 mitochondrial gene). Moreover, it differentiates from other blue Haslea species by the presence of a thin central bar, which has been previously reported in non-blue species like H. pseudostrearia. The complete mitochondrion (36,288 basepairs, bp) and plastid (120,448 bp) genomes of H. nusantara were sequenced and the gene arrangements were compared with other diatom genomes. Phylogeny analyses established using rbcL indicated that H. nusantara is included in the blue Haslea cluster and close to a blue Haslea sp. found in Canary Islands (H. silbo sp. ined.).Conclusions – All investigations carried out in this study show that H. nusantara is a new blue-pigmented species, which belongs to the blue Haslea clade, with an exceptional geographic distribution in the Southern Hemisphere.