The toxic, Harmful Algal Blooms (HABs) caused by the Cochlodinium polykrikoides have a serious impact on the coastal waters of Korea. In this study, the acoustic detection system was developed for rapid HABs detection, based on the acoustic backscattering properties of the C. polykrikoides. The developed system was mainly composed of a pulser-receiver board, a signal processor board, a control board, a network board, a power board, ultrasonic sensors (3.5 and 5.0 MHz), an environmental sensor, GPS, and a land-based control unit. To evaluate the performance of the system, a trail was done at a laboratory, and two in situ trials were conducted: (1) when there was no red tide, and (2) when there was red tide. In the laboratory evaluation, the system performed well in accordance with the number of C. polykrikoides in the received level. Second, under the condition when there was no red tide in the field, there was a good correlation between the acoustic data and sampling data. Finally, under the condition when there was red tide in the field, the system successfully worked at various densities in accordance with the number of C. polykrikoides, and the results corresponded with the sampling data and monitoring result of NFRDI (National Fisheries Research & Development Institute). From the laboratory and field evaluations, the developed acoustic detection system for early detecting HABs has demonstrated that it could be a significant system to monitor the occurrence of HABs in coastal regions.