SNARE proteins function as specificity determinants in all eukaryotic vesicle-mediated transport pathways. Although the intra-erythrocytic parasite Plasmodium falciparum is known to target nuclear-encoded proteins via transport vesicles to several destinations within and beyond its plasma membrane, little is known about the role of SNARE proteins in these unusual trafficking pathways. In this study, we identified and compared the subunit structure of P. falciparum homologues of SNAREs (PfSNAREs) with their complements in mammals, and determined the subcellular localizations of some family members. A comprehensive bioinformatics analysis of the P. falciparum genome revealed 18 SNARE-like proteins that could be classified into five main phylogenetic groups: membrin-like, Bet1-like, VAMP-like, syntaxin5-like, and a P. falciparum-specific syntaxin-like subfamily. Unique to some PfSNARE proteins were presence of atypical amino acid residues at the "0" layer position, presence of up to two transmembrane segments, and frequent occurrence of low-complexity regions. Subcellular distribution of green fluorescence protein (GFP)-tagged P. falciparum SNARE orthologues indicates that PfSyn5p and PfSec22p are partly associated to ER and Golgi compartments, and to other punctuated structures within the parasite plasma membrane. Our data confirms of a conserved SNARE-mediated anterograde transport system in the parasite and argues against any involvement of these two SNAREs in vesicular trafficking within the host cell compartment.