Nitrogen is an essential mineral nutrient and it is often transported within living organisms in its reduced form, as amino acids. Transport of amino acids across cellular membranes requires proteins, and here we report the phylogenetic analysis across taxa of two amino acid transporter families, the amino acid permeases (AAPs) and the lysine–histidine-like transporters (LHTs). We found that the two transporter families form two distinct groups in plants supporting the concept that both are essential. AAP transporters seem to be restricted to land plants. They were found in
Selaginella moellendorffii
and
Physcomitrella patens
but not in Chlorophyte, Charophyte, or Rhodophyte algae. AAPs were strongly represented in vascular plants, consistent with their major function in phloem (vascular tissue) loading of amino acids for sink nitrogen supply. LHTs on the other hand appeared prior to land plants. LHTs were not found in chlorophyte algae
Chlamydomonas reinhardtii
and
Volvox carterii
. However, the characean alga
Klebsormidium flaccidum
encodes KfLHT13 and phylogenetic analysis indicates that it is basal to land plant LHTs. This is consistent with the hypothesis that characean algae are ancestral to land plants. LHTs were also found in both
S. moellendorffii
and
P. patens
as well as in monocots and eudicots. To date, AAPs and LHTs have mainly been characterized in
Arabidopsis
(eudicots) and these studies provide clues to the functions of the newly identified homologs