This study presents the establishment of an integrated multi-trophic aquaculture (IMTA) system in the tropical open waters of southern Cebu, Philippines using a combination of locally available species, namely donkey’s ear abalone (Haliotis asinina) as fed species and seaweeds (Gracilaria heteroclada and Eucheuma denticulatum) as inorganic extractive species. The culture of Caulerpa lentillifera as a biofilter did not work in the open sea cultivation system using baskets. Monthly measurements of shell length, width and body weight of the cultured abalones, together with in situ measurements of physicochemical parameters to assess any changes in water quality, mainly nitrate, nitrite, ammonia and phosphate, were conducted over a year period from February 2013 to January 2014 in three designated stations (Abalone, Seaweed and Control Stations) at three different depths (surface, middle and bottom).Cage culture of abalone side by side with seaweeds in the open sea did not result in any significant water quality disturbance in the area—at least not in the current volume of caged abalones being used. Of the four inorganic compounds monitored in the field, nitrate and ammonia in the Seaweed Station were shown to have relatively lower year-round average values when compared with the Abalone Station, although in the case of nitrate, it was higher in the Control Station compared with the abalone and Seaweed Stations. Although this difference was not significant, it shows the red seaweeds, G. heteroclada and E. denticulatum, to be functioning as a natural filter for these two nutrients. In contrast, nitrite, and phosphate concentrations were not reduced indicating that the seaweeds were not effective biofilter for these two nutrients.The two-month old hatchery-bred donkey’s ear abalones can grow to a size of 53.8×28.2mm (L×W) and body weight of 37.8g after a period of 12 months. Any expansion of the farm into a much larger commercial-scale farm will have to be complimented with seaweeds stocked around it if only to mitigate possible build-up of excess inorganic wastes—to serve as both a natural filter and as a source of natural feed. The potential use of an organic extractive species has to be further studied under farm condition to achieve its full potential as an IMTA species.