Gene and protein sequences of major surface proteins (MSP) 1a and 4 of Anaplasma marginale (Rickettsiales: Anaplasmataceae) were used to infer phylogenetic relationships between New World isolates from Argentina, Brazil, Mexico and the United States. Seventeen isolates of A. marginale plus two outgroup taxa (A. centrale and A. ovis) were used for maximum-parsimony analysis of MSP4, while 20 isolates were used for phylogenetic analysis of MSP1a. msp4 analysis provided strong bootstrap support for a Latin American clade and, within this clade, support was detected for Mexican and South American clades. Isolates of A. marginale from the United States also grouped into two clades from the southern (isolates from Florida, Mississippi, and Virginia) and west-central (isolates from California, Idaho, Illinois, Oklahoma, and Texas) states. Although little phylogeographic resolution was detected within these higher clades, msp4 sequences appear to be a good genetic marker for inferring phylogeographic patterns of A. marginale isolates. In contrast to the phylogeographic resolution provided by msp4, MSP1a DNA and protein sequence were quite variable and did not provide phylogeographic resolution. Most variation in MSP1a sequences appeared unique to a given isolate and similar DNA sequence variation in msp1alpha was detected within isolates from Idaho and Florida and from Idaho and Argentina. The results of these studies demonstrated that msp4 provided phylogenetic information on the evolution of A. marginale isolates. In contrast MSP1a sequences appeared to be rapidly evolving and these sequences may provide phylogeographic information only when numerous isolate MSP1a sequences are analyzed from a geographic area.