The increase in the number of music files in smart phone and MP3 player makes it difficult to find the music files which people want. So, Query-by-Singing/Humming (QbSH) systems have been developed to retrieve music from a user's humming or singing without having to know detailed information about the title or singer of song. Most previous researches on QbSH have been conducted using musical instrument digital interface (MIDI) files as reference songs. However, the production of MIDI files is a time-consuming process. In addition, more and more music files are newly published with the development of music market. Consequently, the method of using the more common MPEG-1 audio layer 3 (MP3) files for reference songs is considered as an alternative. However, there is little previous research on QbSH with MP3 files because an MP3 file has a different waveform due to background music and multiple (polyphonic) melodies compared to the humming/singing query. To overcome these problems, we propose a new QbSH method using MP3 files on mobile device. This research is novel in four ways. First, this is the first research on QbSH using MP3 files as reference songs. Second, the start and end positions on the MP3 file to be matched are estimated by using multi-layered perceptron (MLP) prior to performing the matching with humming/singing query file. Third, for more accurate results, four MLPs are used, which produce the start and end positions for dynamic time warping (DTW) matching algorithm, and those for chroma-based DTW algorithm, respectively. Fourth, two matching scores by the DTW and chroma-based DTW algorithms are combined by using PRODUCT rule, through which a higher matching accuracy is obtained. Experimental results with AFA MP3 database show that the accuracy (Top 1 accuracy of 98%, with an MRR of 0.989) of the proposed method is much higher than that of other methods. We also showed the effectiveness of the proposed system on consumer mobile device.