In this work, we present a compact and ultrasensitive bio-molecule sensor based on fiber specklegram, achieving a DNA detection sensitivity of 10−16 M. To our knowledge, the new device is the most sensitive fiber-optic DNA sensor reported to date. Importantly, the well-known temperature cross-sensitivity issue in many fiber-optic devices has been entirely removed by the introduction of a reference fiber-optic channel embedded in microfluidic channels. In the experiment, we demonstrate label-free DNA hybridization detection at different concentrations, where normalized intensity inner product of the collected specklegrams are calculated and used for determining the DNA concentration. The result shows the exact ssDNA concentration can be precisely determined with a single experiment in 60 min. The new fiber sensor presents distinctive advantages over traditional bio-sensors in terms of sensitivity, precision and cost, which may find many practical applications in health and medicine, e.g., point-of-care testing and disease diagnosis.