Changes in the genome of an organism can cause changes in phenotype. Its phenotype can then determine how well-suited the organism is to its environment. The hologenome concept expands this view by suggesting instead, that it is not only the host genome at play in natural selection, but also the genome of endosymbiotic microorganisms (viruses, bacteria, and fungi) associated with their hosts. The concept is an area of growing interest. It directs the study of biology from an individual-centric approach to one that is more community-centric. This approach opens more opportunities to carefully examine host-community interactions and strategies to ensure a balance between counterparts. However, more intriguing is the potential that the hologenome concept may provide a glimpse into the biological mechanisms of speciation. This paper is a literature review presenting cases in endosymbiont interactions that affect reproductive competence of host and hence, may be an important mechanism of speciation.