The synaptonemal complex is a protein which forms between homolgous chromosomes. The synaptonemal complex begins to form during the zygotene phase of Prophase I in Meiosis and is complete in the pachytene phase. Acting like a 'zipper' it holds the homologous chromosomes together, aligning them perfectly. After complete synapsis, crossing over occurs and in the diplotene phase, where the chiasma is visible, the synaptonemal complex 'unzips' and disappears.
<ref>Hartl DL and Jones EW (2009) Genetics: Analysis of Genes and Genomes, Seventh Edition, USA, Jones and Bartlett Publishers</ref>