Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Triangle pose challenges to biogeographers and resource managers. Comparative phylogeography provides a powerful tool to test biogeographic hypotheses evoked to explain species richness in the Coral Triangle. It can also be used to delineate management units for marine resources. After about a decade of phylogeographical studies, patterns for the Coral Triangle are emerging. Broad connectivity in some species support the notion that larvae have maintained gene flow among distant populations for long periods. Other phylogeographic patterns suggest vicariant events resulting from Pleistocene sea level fluctuations, which have, at least occasionally, resulted in speciation. Divergence dates ranging back to the Miocene suggest that changing land configurations may have precipitated an explosion of species diversification. A synthesis of the marine phylogeographic studies reveals repeated patterns that corroborate hypothesized biogeographic processes and suggest improved management schemes for marine resources. 1. Introduction The Coral Triangle is well recognized as the global apogee of marine biodiversity, with species richness incrementally decreasing from this region eastward across the Pacific Ocean and westward across the Indian Ocean [1, 2]. This center encompasses much of Indonesia, Malaysia, the Philippines, Brunei, Timor L’Este, Papua New Guinea, and the Solomon Islands and is also variously referred to as the East Indies Triangle (e.g., [3–5]), the Indonesian and Philippine Region [6], the Indo-Malay-Philippine Archipelago [7, 8], and a variety of other names [2]. It has also been referred to as the Indo-Australian Archipelago (e.g., [9, 10]) although this is a misnomer for the Coral Triangle biodiversity hotspot, since it does not include Australia [1] and has geological origins transcending Eurasian and Indian‐Australian tectonic elements [11]. In addition to its biodiversity reputation, the Coral Triangle is also unfortunately well known for peaks in threats to marine biodiversity, particularly for reef-building corals and coral reef fishes [12–14] and the need for improved marine resource management [1]. From a geological perspective, the Coral Triangle hotspot is relatively young [15]. Throughout the Paleogene ( 65–23？mya), tropical ocean formed an essentially continuous belt around the globe, with the Atlantic and Pacific basins connected by the Tethys Sea. During much of this time, the global center of marine biodiversity was found in the western
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