G protein-coupled receptors (GPCR) are used ubiquitously and widely for signal transduction across the plasma membrane. The ligands for GPCRs are structurally diverse and include peptides, odorants, photon, ions and lipids. It is thought that GPCRs evolved by gene duplication and mutational events that diversified the ligand binding and signaling properties, thereby resulting in paralogues in various organisms. Genomic sequencing efforts of various organisms indicate that GPCRs evolved very early in evolution; for example, unicellular eukaryotes use GPCRs for mating, differentiation and sporulation responses and prokarotes utilize these receptors for phototransduction, as exemplified by the bacteriorhodopsin, a photon sensor. Many GPCRs fall into subfamilies, usually determined by structural similarity to their ligands. Bioactive lipids such as lysophospholipids, eicosanoids, ether lipids and endocannabinoids, which are produced widely in evolution, also signal through GPCRs. Thus, distinct subfamilies of bioactive lipid GPCRs, such as prostanoid receptors, lysophosphatidic, sphingosine 1-phosphate, leukotrienes, hydroxy fatty acids, endocannabinoids and ether lipids exist in the mammalian genome. With the increasing availability of genomic information throughout the phylogenetic tree, orthologues of bioactive lipid receptors are found in the genomes of vertebrates and chordates but not in worms, flies or other lower organisms. This is in contrast to GPCRs for biogenic amines and polypeptide growth factors, which are conserved in invertebrates as well. Thus, it appears that with the evolution of chordates, lipids may have acquired novel roles in cell-cell communication events via GPCRs. This hypothesis will be discussed using the prostanoid and lysophospholipid signaling systems. Since such bioactive lipids play critical roles in immune, vascular and nervous systems, this suggests that lipid metabolite signaling via the GPCRs co-evolved with the development of sophisticated vascular, immune and nervous systems in chordates and vertebrates.