Diatoms are single-celled algaes that make photonic-crystal-like silica shells or frustules with hierarchical micro-& nano-scale features consisting of two-dimensional periodic pores. In this paper, we present an innovative label-free optical sensor based on a biological-plasmonic hybrid nanostructure by self-assembling silver (Ag) nanoparticles into diatom frustules. The photonic-crystal-like diatom frustules provide a spatially confined electric field with enhanced intensity that can form hybrid photonic-plasmonic modes through the optical coupling with Ag nanoparticles. The experimental results demonstrate 4-6× and 9-12× improvement of sensitivities to detect the Raman dye for resonance and nonresonance SERS sensing, respectively.