Apicomplexans are single celled eukaryotes and parasites that cause veterinarian and human diseases. Important human diseases caused by these parasites include malaria, cryptosporidiosis, toxoplasmosis and babesiosis. Most members of the phylum (with the exception of Cryptosporidium) are characterized by the presence of a non-photosynthetic plastid called the apicoplast. The apicoplast is derived from a secondary endosymbiosis event where a red algal endosymbiont was engulfed by a heterotrophic organism that resulted in the four membranes that now surround the apicoplast. Although the organelle has lost its photosynthetic properties, the apicoplast is the location of important biochemical processes including isoprenoid, fatty acid and heme biosynthesis. The apicoplast's divergent origin and its essential biochemical processes suggest the organelle as an ideal therapeutic target. It is estimated that almost 500 endosymbiont genes were transferred to the host's nucleus. Consequently, these now nuclear encoded apicoplast proteins must be transported back across the four membranes of the apicoplast to reach their site of action. Previous studies have demonstrated a series of distinct translocons that are dedicated to transport across each of the organelle's multiple membranes. Here we focus on a system that is derived from the endoplasmic reticulum associated degradation (ERAD) pathway and has been repurposed for import across the second outermost membrane or periplastid membrane of the apicoplast. While previous research has demonstrated several components of the apicoplast. While previous research has demonstrated several components of the apicoplast ERAD machinery as critical for import, the crucial ubiquitin modifier typically associated with the ERAD machinery remained elusive. My dissertation provides the first evidence of an apcioplast specific ubiquitin-like protein and defines its function by generating a conditional mutant and establishing complementation which allowed definitive analysis to characterize the protein. My finding revealed that the apicoplast specific ubiquitin-like protein is significantly different from any known ubiquitin-like protein, critical for parasite viability and essential for protein import across the periplastid membrane. I demonstrate that CDC48, another component of the ERAD machinery that may interact with ubiquitin, is crucial for apicoplast protein import across the periplastid membrane and apicoplast biogenesis. We identify additional components of the apicoplast ubiquitin-like machinery including candidate ubiquitin ligases and deubiquitinases.