Molecularly imprinted nanoparticles are cross-linked polymer colloids containing tailor-made molecular recognition sites. In this study, molecularly imprinted nanoparticles were easily encapsulated within polymer nanofibers using an electrospinning technique to produce a new type of molecular recognition material. Poly(ethylene terephthalate) (PET) was used as the supporting nanofibers matrix to encapsulate theophylline and 17 beta-estradiol imprinted nanoparticles. The composite nanofibers had an average diameter of 150-300 nm, depending on the content of molecularly imprinted nanoparticles. For the theophylline and 17 beta-estradiol imprinted polymers, an optimal loading of molecularly imprinted nanoparticles was 25-37.5 wt % based on PET. The composite nanofibers prepared under these conditions had a well-defined morphology and displayed the best selective target recognition. Our approach of electrospinning-for-molecularly imprinted nanoparticles-encapsulation has unique advantages and opens new application opportunities for molecularly imprinted nanoparticles and electrospun nanofibers.