Florist's chrysanthemum (Chrysanthemum morifolium Ramat.) belongs to the Asteraceae family and represents the second most important floricultural crop in the world. Most genotypes are sensitive to aphids and infestations can lower quality and cause transmission of viruses. The protease inhibitor Sea Anemone Equistatin (SAE) carries three domains responsible for the inhibition of both cysteine and aspartic proteases. Artificial diet bioassays showed that SAE is readily toxic when ingested by the pea aphid, Acyrthosiphon pisum, and the cotton aphid, Aphis gossypii. We transformed chrysanthemum genotype 1581 by Agrobacterium tumefaciens-mediated transformation with the SAE gene under the control of the chrysanthemum RbcS promoter to induce aphid resistance. Non-choice leaf disk and whole plant bioassays were carried out to analyze deleterious effects of SAE on population growth and survival of both Myzus persicae and A. gossypii. After 7 days, M. persicae populations on specific transgenic lines were up to 69% smaller relative to control populations in a whole plant bioassay. The mortality of cotton aphids was 11% on control lines and up to 32% on transgenic lines after 5 days. The results show that SAE may be a promising agent for the control of some aphid species in transgenic plants.