The mechanisms for the precise regulatory control of genes have long been a question in the field of molecular biology. While traditional views of gene regulation focus on the cis-regulatory elements and transcription factors involved, a new field of study focuses on the trans-regulatory functions of non-coding RNAs. In recent years, both small and long non-coding RNAs have been recognized as important elements in the regulation of many different cellular processes, however, the identification and characterization of long non-coding RNAs is still in its infancy. The Bithorax Hox Gene Complex of Drosophila melanogaster has long been known to contain a multitude of long non-coding RNAs of unknown function. While many of the cis-regulatory mechanisms of this historical complex have since been worked out, many of the non-coding RNAs remain mysterious. With the advent of new techniques and a fresh RNA-centric viewpoint, several researchers have recently returned to the Bithorax Complex to study the vast non-coding transcription that pervades its inter- and intragenic regions. These studies reveal that these non-coding RNAs act in trans as important regulators of the protein-coding Hox gene, Ultrabithorax.