In this study the local two-phase heat transfer coefficients were obtained using wall temperature measurements and fluid saturation temperatures in a rectangular high-aspect-ratio polydimethylsiloxane (PDMS) microchannel with a hydraulic diameter of 192 μm. The experiments used FC-72 liquid with a mass flux of 7.37 kg m−2s−1 and various heat fluxes ranging between 3.34 and 61.95 kW m−2. Fluid saturation temperatures were determined by interpolating pressure measurements obtained with integrated silicon ceramic-based pressure sensors located near the inlet and outlet of the microchannel. The hydrodynamic and flow boiling characteristics of the microchannel were monitored using high frequency and high spatial resolution infrared thermography, with heat transfer coefficients obtained as a function of axial position, lateral position and time and at the inlet, middle and outlet sections of the microchannel. This enabled the effect of heat flux on local temperature, flow boiling heat transfer coefficient distribution and two-phase pressure drop to be determined. These results suggest that the two-phase heat transfer coefficient does not increase monotonically with the heat flux, and actually decreases under certain conditions. This work identifies that the heat transfer coefficient depends on the range of the heat flux and is correlated with vapour-liquid dynamics and liquid film thinning resulting in suspected dryout, observed simultaneously with the temperature measurements. The simultaneous application of high speed thermography and flow visualization has enabled uniquely detailed information to be obtained that is useful to a more detailed understanding of two-phase flow and bubble dynamics.