The southeastern USA hosts the largest nesting concentration of loggerhead turtles Caretta caretta in the Atlantic. Regionally significant nesting also occurs along the Caribbean coast of Mexico, in Cuba, and in the Bahamas. Previous studies of North Atlantic loggerhead turtle rookeries based on a 380 bp fragment of the mitochondrial control region supported recognition of 8 demographically independent nesting populations (management units) in the Northwest Atlantic in addition to Cape Verde in the eastern Atlantic. Recent analysis of expanded mitochondrial control region sequences revealed additional genetic diversity and increased population structure between western and eastern Atlantic loggerhead turtle rookeries. We sequenced an 817 bp mitochondrial DNA fragment in 2427 samples from nesting beaches in the southeastern USA, Cay Sal Bank, Bahamas, and Quintana Roo, Mexico. Pairwise F-ST comparisons, pairwise exact tests of population differentiation, and analysis of molecular variance support previously proposed management unit designations and additionally indicate that southeastern and southwestern Florida rookeries should be recognized as distinct management units. Therefore, Northwest Atlantic loggerhead turtle rookeries can be subdivided into 10 management units, corresponding to the beaches from (1) Virginia through northeastern Florida, (2) central eastern Florida, (3) southeastern Florida, (4) Dry Tortugas, Florida, (5) Cay Sal, Bahamas, (6) southwestern Cuba, (7) Quintana Roo, Mexico, (8) southwestern Florida, (9) central western Florida, and (10) northwestern Florida. We confirmed increased resolution of stock structure between many Northwest Atlantic management units and the Cape Verde rookery with the expanded control region haplotypes.