Optofluidic devices are particularly well-suited for biological and chemical sensing. Especially, nanophotonic sensors employed in optofluidics have greatly overcome the limitations of conventional optical sensors in terms of size, sensitivity, specificity, tunability, photostability, and in vivo applicability. [1] Equally important, microfluidic devices enable facile delivery of sample solution to the sensing region and allow for high throughput detection. However, the limit of mass transport imposed by the laminar flow inside the microfluidic channel dictates the sensitivity and throughput of optofluidic devices. [2] In past years, various optofluidic devices have been developed using microring resonators, [3] metamaterials, [4] surface plasmon resonance (SPR), [5] and surfaceenhanced Raman scattering (SERS). [6] As a vibrational spectroscopic technique, SERS can provide specific information about the molecular structure by the strong local optical field enhancement generated by plasmonic nanoparticles (NPs) or nanostructures. [7] Most published optofluidic-SERS results were obtained utilizing either 1) colloidal metallic NPs flowing inside microfluidic channels, or 2) SERS-active plasmonic nanostructures fabricated on the surface of the microfluidic channels to provide the necessary SERS enhancement factors (EFs). Plasmonic NPs, primarily based on silver (Ag) or gold (Au), such as colloidal metallic NPs, [8] nanorods, [9] nanostars, [10] core-shell NPs, [11] and Surface-enhanced Raman scattering (SERS) sensing in microfluidic devices, namely optofluidic-SERS, suffers an intrinsic tradeoff between mass transport and hot spot density, both of which are required for ultrasensitive detection. To overcome this compromise, photonic crystal-enhanced plasmonic mesocapsules are synthesized, utilizing diatom biosilica decorated with in-situ growth silver nanoparticles (Ag NPs). In the optofluidic-SERS testing of this study, 100× higher enhancement factors and more than 1,000× better detection limit are achieved compared with traditional colloidal Ag NPs, the improvement of which is attributed to unique properties of the mesocapsules. First, the porous diatom biosilica frustules serve as carrier capsules for high density Ag NPs that form high density plasmonic hot-spots. Second, the submicron-pores embedded in the frustule walls not only create a large surface-to-volume ratio allowing for effective analyte capture, but also enhance the local optical field through the photonic crystal effect. Last, the mesocapsules provide effective mixing with analytes as they are flowing inside the microfluidic channel. The reported mesocapsules achieve single molecule detection of Rhodamine 6G in microfluidic devices and are further utilized to detect 1 × 10 −9 m of benzene and chlorobenzene compounds in tap water with near real-time response, which successfully overcomes the constraint of traditional optofluidic sensing.