An antibiotic producing novel Planctomycete strain, designated JC280T, was isolated from the surface of the plant Hydrilla verticillata collected from an alkaline lake (Buffalo lake), University of Hyderabad, Hyderabad, India. The morphological and chemotaxonomic properties of strain JC280T were in agreement with the characteristics of the genus Planctopirus. The cell shape was spherical to ovoid and some were tear drop shaped. The cells were Gram-stain-negative divided by budding presenting stalks and rosette formation and were non-sporulating. Crateriform structures with a sub-polar flagellum were observed. Characteristic polyamines were putrescine and spermidine. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid (PL1), unidentified glycolipids (GL1-2), an unidentified aminophospholipid (APL), and an unidentified lipid (L3). Major (>10%) fatty acids were C16:0, C17:1ω8c, C18:1ω9c, and summed feature-3. Major (88%) respiratory quinone was MK-6 with minor amount (12%) of MK-7. Strain JC280T showed 99.7% 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. To resolve their full taxonomic position, the genome sequence was obtained and compared with the available P. limnophila DSM 3776T genome. The genome sequence of strain JC280T was 5,750,243 bp in size with a total of 4490 protein-coding genes, 66 RNA genes, and 2 CRISPR repeats. Based on whole-genome statistics, ANI value, in silico DDH, diversity of secondary metabolite biosynthetic gene clusters, distinct physiological, biochemical and chemotaxonomic differences, strain JC280T represents a new species in the genus Planctopirus, for which the name Planctopirus hydrillae sp. nov. is proposed. The type strain is JC280T (=KCTC 42880T = LMG 29153T).