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Phylogeography of Hypnea valentiae in India indicates that nuclear ribosomal DNA Internal transcribed spacer-1 (ITS1) sequences had 4.35 x 10-1 Tamura 3-parameter (T3P) pairwise distance between them, which indicate significant evolutionary differences accumulated over time. In comparison, T3P distance between related genera Kappaphycus and Eucheuma was 1.85 x 10-1. In phylogeny reconstruction using Bayesian inference, both the isolates formed a well-supported clade along with the only available accession of this genus at ITS1 locus, indicating affiliation of both the isolates in this genus. The isolate from the west coast was more basal in the phylogram, which suggests phylogenetically primitive position of this population. Newly generated DNA barcodes of the geographic isolates of this native carrageenophyte in this study is expected to be a key in tracing its further dispersal routes, either natural or deliberate. This is the first report on the comparative morphological and molecular assessment of Hypnea from India.