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The sensitivity of fluorescent sensors is crucial for their applications. In this study, we propose a molecularly imprinted polymer (MIP)-coated optical fibre–hybrid waveguide-fibre sensing structure for ultrasensitive fluorescence detection. In such a structure, the MIP coated-hybrid waveguide acts as a sensing probe, and the two co-axially connected optical fibres act as a highly efficient probing light launcher and a fluorescence signal collector, respectively. For the dual-layered waveguide sensing probe, the inner hybrid waveguide core was fabricated using a hollow quartz nanoparticle–hybridized polymer composite with a low refractive index, and the outer MIP coating layer possesses a high refractive index. Simulations showed that this dual-layer configuration can cause light propagation from the waveguide core to the MIP sensing layer with an efficiency of 98%, which is essential for detection. To validate this concept, we adopted a popular fluorescent dye, rhodamine B, to evaluate the sensing characteristics of the proposed system. We achieved an extremely low limit of detection of approximately 1.3 × 10−19 g ml−1 (approximately 0.27 aM). [ABSTRACT FROM AUTHOR]