The whispering gallery mode (WGM) based micro-bottle resonator (MBR) sensor has been proposed and demonstrated for relative humidity measurement by using an agarose gel as a transducer. MBR was fabricated by using a soften- and-compress method to form a 190 μm bulge bottle. The micro-bottle was optically excited by a 3 μm tapered fiber and it exhibits a resonance with a Q factor in an order of 105. The agarose coated MBR produces a good sensing response towards humidity with the sensitivity of 0.107 dB/%RH and linearity of 99.614%. The agarose hydrophilic nature and its changing porosity and refractive index with increasing relative humidity made the coated MBR structure to be more sensitive than the uncoated structure. This humidity sensor has a simple fabrication and is showing good sensitivity, linearity, resolution, response time and operational in a wide humidity range.