Using methods of pulsed laser ablation from a silicon target in helium (He)-nitrogen (N2) gas mixtures maintained at reduced pressures (0.5–5 Torr), we fabricated substrate-supported silicon (Si) nanocrystal-based films exhibiting a strong photoluminescence (PL) emission, which depended on the He/N2 ratio. We show that, in the case of ablation in pure He gas, Si nanocrystals exhibit PL bands centered in the “red - near infrared” (maximum at 760 nm) and “green” (centered at 550 nm) spectral regions, which can be attributed to quantum-confined excitonic states in small Si nanocrystals and to local electronic states in amorphous silicon suboxide (a-SiOx) coating, respectively, while the addition of N2 leads to the generation of an intense “green-yellow” PL band centered at 580 nm. The origin of the latter band is attributed to a radiative recombination in amorphous oxynitride (a-SiNxOy) coating of Si nanocrystals. PL transients of Si nanocrystals with SiOx and a-SiNxOy coatings demonstrate nonexponential decays in the micro- and submicrosecond time scales with rates depending on nitrogen content in the mixture. After milling by ultrasound and dispersing in water, Si nanocrystals can be used as efficient non-toxic markers for bioimaging, while the observed spectral tailoring effect makes possible an adjustment of the PL emission of such markers to a concrete bioimaging task.