A trial was carried out to compare the growth performance, body composition and apparent digestibility coefficients (ADC) of diets by seabass, with an initial weight of 13.5 g, fed diets including fish meal (68.6 % of the dietary protein) or soybean meal (65.6 % of the dietary protein) as the main protein sources. Microbial phytase was added to the soybean meal based diet (1 000 and 2 000 IU·kg−1) and to the fish meal based diet (2 000 IU·kg−1) in order to study its effect on phosphorus utilisation. Results of this trial showed that growth rate, feed conversion and nitrogen retention were significantly better in fish fed the fish meal based diet. Energy retention was similar in both groups. ADC of protein were similar among groups. ADC of phosphorus was significantly higher in the fish meal based diet (63 %) than in the soybean meal based diet (25 %). Supplementation of the fish meal based diet with microbial phytase did not improve the ADC of phosphorus, while in the soybean meal based diet the inclusion of 1 000 and 2 000 IU·kg−1 of microbial phytase significantly increased the ADC of phosphorus to 71.5 % and 79.8 %, respectively. It is concluded that for practical purposes supplementation of diets with microbial phytase may prove valuable in diets including high levels of plant feedstuffs.