Selective breeding uses the phenotype of the DNA, the way it is expressed, to select good traits, whereas GMO is modified at the level of the genes with new genes inserted to give the desirable characteristics associated with those genes. The species used in selective breeding have a ubiquitous evolutionary origin.
The gene can be taken from any species. The genes used to make GMO plants or animals must be secluded from other organisms, which does not take place in selective breeding. Unlike selective breeding, highly knowledgable technicians are necessary for the GMO process. In contrast, genetic engineering is a costly process, while selective breeding is a less expensive method.