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In this study, we evaluate and compare the pulse shape discrimination (PSD) performance of multipixel photon counters (MPPCs, also known as silicon photomultiphers - SiPMs) with that of a typical photomultiplier tube (PMT) when testing using CsI(Tl) scintillators. We use the charge comparison method, whereby we discriminate different types of particles by the ratio of charges integrated within two time-gates (the delayed part and the entire digitized waveform). For a satisfactory PSD performance, a setup should generate many photoelectrons (p.e.) and collect their charges efficiently. The PMT setup generates more p.e. than the MPPC setup does. With the same digitizer and the same long time-gate (the entire digitized waveform), the PMT setup is also better in charge collection. Therefore, the PMT setup demonstrates better PSD performance. We subsequently test the MPPC setup using a new data acquisition (DAQ) system. Using this new DAQ, the long time-gate is extended by nearly four times the length when using the previous digitizer. With this longer time-gate, we collect more p.e. at the tail part of the pulse and almost all the charges of the total collected p.e. Thus, the PSD performance of the MPPC setup is improved significantly. This study also provides an estimation of the short time-gate (the delayed part of the digitized waveform) that can give a satisfactory PSD performance without an extensive analysis to optimize this gate.