Two issues that have captured the attention of tropical plant evolutionary biologists in recent years are the relative role of long distance dispersal (LDD) over vicariance in determining plant distributions and debate about the extent that Quaternary climatic changes affected tropical species. Propagules of some mangrove species are assumed to be capable of LDD due to their ability to float and survive for long periods of time in salt water. Mangrove species responded to glaciations with a contraction of their range. Thus, widespread mangrove species are an ideal system to study LDD and recolonization in the tropics. We present phylogenetic and phylogeographic analyses based on internal transcribed spacers region (ITS) sequences, chloroplast DNA (cpDNA), and amplified fragment length polymorphisms (AFLPs) of genomic DNA that demonstrate recent LDD across the Atlantic, rejecting the hypothesis of vicariance for the widespread distribution of the black mangrove (Avicennia germinans). Northern latitude populations likely became extinct during the late Quaternary due to frosts and aridification; these locations were recolonized afterward from southern populations. In some low latitude regions populations went extinct or were drastically reduced during the Quaternary because of lack of suitable habitat as sea levels changed. Our analyses show that low latitude Pacific populations of A. germinans harbor more diversity and reveal deeper divergence than Atlantic populations. Implications for our understanding of phylogeography of tropical species are discussed.