Generally, nanodendrite synthesis is chemical mediated and expensive. The biogenesis of such hierarchical structures is still in its nascent stage. The present study aimed at exploiting the nanoporous frustules of Halamphora subturgida, as a source of biosilica for the biosynthesis and stabilization of conjugate nanodendrites of silica and silver. These minute diatom frustules when exposed to 9 mM of silver nitrate solution, a highly crystalline nanohybride dendrites were synthesized. The nanohybrid dendrite synthesis was initially confirmed by the formation of greyish-brown frustules after 72 h of exposure. The composite dendrites were thoroughly characterized by standard techniques. Electron microscopic images illustrated that the process began with the formation of isotropic hybrid nanospheres with an internal diameter of 20 nm and continued to develop anisotropic nanocrystals with time. The nanodendrites externally formed on the siliceous frustules, acting as a template for the former. They were characterized by distinct 100 nm wide and 1–2 µm long trunks and 70–100 nm wide and 220–220 nm long branches on either side of the trunk. The optical measurement revealed the fluorescence property of the nanostructures owing to the photoluminescent efficiency of the frustules. Both the externally derived hybrid nanodendrites and internally synthesized nanospheres possessed superior stability in the suspension with a zeta potential value of − 35.7 mV and − 24.8 mV, respectively. Thus, this method is eco-friendly and provides a new dimension for nanodendrite synthesis with minimal cost and maximal yield compared to its non-biologically synthesized counterparts that involve several other drawbacks like chemical hazards and high energy consumption. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.