With expansion of hydroponic culture, demand for subsrate materials also has increased and necessity for more study to find the best substrate according to the plant characteristics seems to be necessary. For this purpose, a study was carried out on chrysanthemum cv puma using a factorial design with two factors, first a different substrate (cocopeat: perlite, 0:100, 25:75, 50:50, 75:25, 100:0) and second, a culture system (aquaponic and hydroponic) with compeletly randomized design and three replicates for 5 months. Results of ANOVA showed that the culture system and substrate form and their interaction has a significant (p<0.01) effect on chrysanthemum quantity and quality characteristics. According to the results of this study, in hydroponic system, vegetative growth characteristics of plants were higher compared to aquaponic. In substrate with 100% pelite, fresh and dry weight of roots and shoots were the lowest, whereas plants in 25% perlite+75% cocopeat had the highest fresh and dry weight of roots and shoots. Thus, the substrate ratio of 25% perlite+75% cocopeat was the best substrate for vegetative growth. There was a significant difference between hydroponic and aquaponic in reproductive characteristics of plants e.g., flower number per plant, flower number on one shoot, flower bud number, quality index and length of king flower. Plants in hydroponic system had the highest flower in the substrate ratio of 50% perlite+50%cocopeat, although this increment in flower number caused the reduction of flowers quality compared to other cocopeat contained substrates, whereas, in aquaponic system the highest flower number of plants was observed in 100% perlite substrate. Generally, plants in the substrate with mixture of cocopeat and perlite especially in the higher ratios of cocopeat had the best growth which is related to good physical characteristics of perlite and good physicochemical characteristics of cocopeat especially higher water and nutrient maintenance of cocopeat.