PEX genes encode the protein machinery (peroxins) required for proper peroxisome assembly. Peroxisomal membrane proteins are imported through at least two routes, one of which depends on interaction between peroxin 19 and peroxin 3, while the other is required for import of peroxin 3, either of which may occur without the import of matrix (lumen) enzymes, which possess the peroxisomal targeting signal PTS1 or PTS2 as previously discussed.  Elongation of the peroxisome membrane and the final fission of the organelle are regulated by Pex11p.
Genes that encode peroxin proteins include: PEX1, PEX2 (PXMP3), PEX3, PEX5, PEX6, PEX7, PEX9, PEX10, PEX11A, PEX11B, PEX11G, PEX12, PEX13, PEX14, PEX16, PEX19, PEX26, PEX28, PEX30, and PEX31. Between organisms, PEX numbering and function can differ.