We have developed a sensitive optofluidic cytometer to investigate microscale particles. The flow cytometer is comprised of a microchannel that has a set of chevron-shaped grooves. Conducted by the chevrons, two sheath streams focus the core stream in the center of the microchannel three-dimensionally. The optofluidic cytometer is equipped with the new generation of photodetectors, multi-pixel photon counter (MPPC). MPPCs are highly sensitive photodetectors with extremely small footprint that deliver high gain values of up to 107. We have employed a MPPC as the photodetector unit in our cytometer. Two different sizes of high intensity fluorescent microspheres are run through the cytometer. The signal outputs from both particles are collected using a data acquisition unit for further statistical analysis. The emission light produced by samples is received by a multimode fiber that is located in 135-degree with respect to the excitation fiber. The effect of particle size on the range of collected signal output is investigated by observing the forward scattering emission from samples. Statistical analysis of collected signal proved that for 10.2 µm particles, the peak height, width, and consequently area are larger than 3.2 µm particles. Finally using a 35 mW diode laser three types of algae are characterized in the flow cytometer based on their sizes. COMSOL software was employed to simulate the concentration distribution along the microchannel.