Islands have long been recognized for the numerous endemic species they support, and genomics tools enable rigorous tests of evolutionary processes generating endemism and diversity in island systems. Unfortunately, island diversity is subject to numerous anthropogenic threats, especially the introduction of invasive species. Here, I used data from two Argentine ant eradication programs on Santa Cruz Island and San Clemente Island, California, to examine how Argentine ant introduction affects native ant richness and shifts the composition of native ant assemblages. I found that the arrival of the Argentine ant in previously uninvaded plots coincided with large and rapid declines in ant species richness, and shifts in species composition. I also used genomics data generated through high-throughput sequencing of ultraconserved elements to (i) examine the evolutionary processes that result in endemism within four insular endemic ant taxa on the southern California Channel Islands and (ii) to conduct a multi-species comparison of genetic diversity and population genetic structure between island (Santa Cruz Island) and mainland (Lompoc Valley, California) populations of nine ant species to test for reduced levels of diversity and capacity for dispersal in insular ant populations. I found that endemism within ants on the southern Channel Islands results from both allochthonous and autochthonous evolutionary processes on multiple islands and within a single island. I also found that island populations do not differ significantly from mainland populations with respect to estimates of genetic diversity, and that mainland populations exhibit higher levels of population genetic structure consistent with lower capacities for dispersal within mainland populations. Together these studies illustrate the negative impacts of Argentine ant introductions on these unique insular assemblages, and provide novel insights into the evolutionary processes that generate endemism and genetic diversity within the ant fauna of the California Channel Islands.