Carbon dots (C-dots) are a class of novel fluorescent nanomaterials, which have drawn great attention for their potential applications in bio-nanotechnology. Multicolor C-dots have been synthesized by chemical nitric acid oxidation using the reproducible plant soot as raw material. TEM analysis reveals that the prepared C-dots have an average size of 3.1nm. The C-dots are well dispersed in aqueous solution and are strongly fluorescent under the irradiation of ultra-violet light. X-ray photoelectron spectroscopy characterization demonstrates that the O/C atomic ratio for C-dots change to from 0.207 to 0.436 due to the chemical oxidation process. The photo bleaching experiment reveals that the C-dots show excellent photostability as compared with the conventional organic dyes, fluorescein and rhodamine B. The fluorescence intensity of the C-dots did not change significantly in the pH range of 3–10. To further enhance the fluorescence quantum yield, the C-dots were surface modified with four types of passivation ligands, 4,7,10-trioxa-1,13-tridecanediamine (TTDDA), poly-L-lysine (PLL), cysteine and chitosan and the fluorescence quantum yields of the TTDDA, PLL, cysteine and chitosan passivated C-dots were improved 1.53-, 5.94-, 2.00- and 3.68-fold, respectively. Fourier-transform infrared (FTIR) spectra were employed to characterize the surface groups of the C-dots. The bio-application of the C-dots as fluorescent bio-probes was evaluated in cell imaging and ex vivo fish imaging, which suggests that the C-dots may have potential applications in biolabeling and bioimaging. Display omitted •Using plant soot as the carbon source, multicolor carbon dots were prepared via a facile and effective one-pot chemical oxidation method.•Enhanced photoluminescence was observed when these C-dots were surface modified using various surface passivation agents.•These C-dots have been successfully used for cellular and fish imaging, which may have potential applications in bio-technology.