Secure identification of individual plants by some kind of labels in the field is an important part of many types of horticultural, plant science, and ecological research. This report describes implanted microchips as one method of plant tagging that is reliable, durable, and secure. This technology may be especially useful in long-term experiments involving perennial woody plants. Two methods are described for implanting microchips in citrus trees that would also be applicable to other woody plant species. One method of implanting microchips is demonstrated to have no deleterious effect on citrus tree growth through the first 18 months after implantation into the tree. Since microchips implanted beneath the bark will become more deeply embedded in wood as the plants grow, signal penetration through wood was evaluated and determined to be sufficient for long-term field utility. Implanted microchips are potentially useful for secure tagging of valuable or endangered plant species to deter theft by providing secure and conclusive identification.