A method and apparatus for a Phytoimmune system to manage diseases in fruit trees, in which concomitant in vitro micrografting is used with actively growing plant tissue to create Complex Architecture Plants capable of generating immune, resistance, or tolerance responses to specific targeted plant diseases, such as the bacterial disease Huanglongbing (HLB), also, known as Citrus Greening Disease, and the viral disease Plum Pox Virus (PPV), also known as Sharka disease.