Ion implantation doping and isolation coupled with rapid thermal annealing has played a critical role in the realization of high performance photonic and electronic devices in all mature semiconductor material systems. This is also expected to be the case for the binary III-V nitrides (InN, GaN, and AlN) and their alloys as the epitaxial material quality improves and more advanced device structures are fabricated. In this article, we review the recent developments in implant doping and isolation along with rapid thermal annealing of GaN and the In-containing ternary alloys InGaN and InAlN. In particular, the successful nand p-type doping of GaN by ion implantation of Si and Mg+P, respectively, and subsequent high temperature rapid thermal anneals in excess of 1000 degrees C is reviewed. In the area of implant isolation, N-implantation has been shown to compensate both n- and p-type GaN, N-, and O-implantation effectively compensates InAlN, and InGaN shows limited compensation with either N- or F-implantation. The effects of rapid thermal annealing on unimplanted material are also presented.