Nucleomorphs are the reduced nuclei derived from endosymbionts found in some secondary symbiotic algae. Research into the nucleomorph has provided many insights into its role as a product of secondary endosymbiosis, as well as the resulting genome reduction and gene transfer. Recently developed biological techniques and bioinformatic tools have enabled us to examine the characteristics of nucleomorphs more comprehensively than was previously possible. Moreover, new approaches in synthetic biology have begun to emerge that may provide a valuable platform to study artificial endosymbiosis. Together, these technologies could allow greater insights into the mechanisms and regulation of genomic dynamics within the nucleomorph.