A multilayered nanofibrous microfiltration (MF) membrane system with high flux, low pressure drop, and high retention capability against both bacteria and bacteriophages (a virus model) was developed by impregnating ultrafine cellulose nanowhiskers (diameter about 5 nm) into an electrospun polyacrylonitrile,(PAN) nanofibrous scaffold (fiber diameter about 150 nm) supported by a poly(ethylene terephthalate) (PET) nonwoven substrate (fiber diameter about 20 mu m). The cellulose nanowhiskers were anchored on the PAN nanofiber surface, forming a cross-linked nanostructured mesh with very high surface-to-volume ratio and a negatively charged surface. The mean pore size and pore size distribution of this MP system could be adjusted by the loading of cellulose nanowhiskers, where the resulting membrane not only possessed good mechanical properties but also high surface charge density confirmed by the conductivity titration and zeta potential measurements. The results indicated that a test cellulose nanowhisker-based MP membrane exhibited 16 times higher adsorption capacity against a positively charged dye over a commercial nitrocellulose-based MF membrane. This experimental membrane also showed full retention capability against bacteria, for example, E coli and B. diminuta (log reduction value (LRV) larger than 6) and decent retention against bacteriophage MS2 (LRV larger than 2).