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Mesoporous encapsulation of gold nanorods (GNRs) in a silica shell of controllable thickness (4.5-25.5 nm) was realized through a single-step coating method without any intermediary coating. The dependence of localized surface plasmon resonance (LSPR) extinction spectra of the coated GNRs on the thickness of the silica shell was investigated with both simulation and experiments, which agreed well with each other. It was found that cetyltrimethyl ammonium bromide (CTAB) molecules, which act as surfactants for the GNRs and dissociate in the solution, greatly affect the silica coating. Mesoporous silica-encapsulated GNRs were also shown to be highly biocompatible and stable in bio-environments. Based on LSPR enhanced scattering, mesoporous silica-encapsulated GNRs were utilized for dark field scattering imaging of cancer cells. Biomolecule-conjugated mesoporous silica-encapsulated GNRs were specifically taken up by cancer cells in vitro, justifying their use as effective optical probes for early cancer diagnosis. Mesoporous silica can also be modified with functional groups and conjugated with certain biomolecules for specific labeling on mammalian cells as well as carrying drugs or biomolecules into biological cells.