Antimicrobial peptides naturally occur in a wide range of life forms including bacteria, fungi, plants and animals and represent an important component of their innate immunity systems. These peptides can inhibit the growth of animal and plant pathogenic bacteria and fungi. Designed synthetic peptides based on the structure of naturally occurring peptides have been shown to inhibit the growth of animal and plant pathogenic bacteria and fungi. In this chapter we report the engineering of T. cacao plants to express synthetic peptides and the in planta effects on the damage (necrosis) caused by two important oomycete pathogens of this crop. Theobroma cacao transgenic lines expressing synthetic peptides D5C and pD4E1 exhibited less foliar damage by pathogen Phytophthora capsici and P. palmivora than wild type cacao. We discuss the potential effects of antimicrobial peptides on non-pathogenic symbiotic microorganisms of plants e.g. mychorrizae and endophytes.