A new variant of the diaminopimelate (DAP)/lysine pathway has been recently discovered by identification of an L,L-diaminopimelate aminotransferase (DapL), first in photosynthetic organisms and subsequently in heterotrophic eubacteria and archaea. The enzyme catalyzes the formation of L,L-diaminopimelate (L,L-DAP) from L-2,3,4,5-tetrahydrodipicolinate (THDPA) in one step bypassing the three core enzymes encoded by the dapD, dapC and dapE genes from the classic DAP pathway that exists in E. coli. The phylogenetic distribution of the DapL pathway was examined by analyzing the occurrence of DapL orthologs among the sequenced microbial genomes. Orthologous candidate genes were identified in both the eubacteria and archaea. They clustered into two divergent groups (DapL1, DapL2) sharing approximately 30% amino acid identity. In some species, dapL orthologs were found to lie in a genomic context with other DAP/lysine genes, suggestive of a polycistronic structure. Several DapL candidates were selected for functional analysis by mutant complementation and in vitro kinetic studies. The results show that both DapL1 and DapL2 examples catalyze DAP aminotransfer. In most cases the presence of a dapL ortholog in a species correlated with the absence of genes representing other DAP pathway variants, including dapD, dapC, dapE and ddh (m-DAP dehydrogenase). These results suggest that DapL is required for DAP/lysine biosynthesis. The results from the survey indicate that the DapL pathway is restricted to specific bacterial lineages of eubacteria including the Cyanobacteria, Desulfuromonadales, Firmicutes, Bacteroidetes, Chlamydiae, Spirochaeta, Chloroflexi; and a single archaeal group the Methanobacteriaceae. The finding has further significance in that some DapL-containing species are human pathogens, such as Leptospira interrogans, which is responsible for the disease leptospirosis and Chlamydia trachomatis responsible for a common sexually transmitted disease (STD). The identification of a unique enzyme in these species could provide a target for identification of an specific antibiotic.