There is a critical need for early detection of pathogens in Phalaenopsis orchid due to its high economic value in agriculture. In our previous work , an integrated microfluidic system capable of detecting these pathogens through pathogen-specific ribonucleic acid (RNA) purification and RNA amplification by using reverse transcription loop-mediated-isothermal-amplification (RT-LAMP) was presented. In this study, a buried optical fiber-based detection module was integrated with the microfluidic chip to monitor the RT-LAMP reaction directly on-chip such that in-line optical detection can be realized. Successful RT-LAMP reaction, which amplifies the nucleic acids that yield the precipitate, magnesium pyrophosphate, and therefore increased the turbidity in the LAMP products could be detected optically. Furthermore, a fluorescent dye, calcein, could be also used in our system to detect the fluorescent signals, if necessary. Thus sensitive and fast diagnosis of the pathogens in Phalaenopsis orchids could be successfully achieved by using the integrated microfluidic system.