Epiphytic bacteria from marine macroalgae synthesize enzymes of industrial and biotechnological interest. In this study, we obtained two DNA candidate fragments for lipid-degrading enzymes from the total DNA of Ulva lactuca-associated epiphytic bacteria. First, we evaluated a method for total bacterial DNA isolation from the surface of U. lactuca thalli. Then, we designed sets of primers and used them directly for PCR amplification. The resulting PCR products were sequence-analyzed and used for expression and functional evaluation with the Escherichia coli pBAD-TOPO system. We obtained high molecular weight and good quality total bacterial DNA that served as a template to identify a fragment corresponding to an Acetyl-CoA C-Acetyltransferase (or Thiolase), and a candidate fragment for a versatile “true” lipase. We expressed the possible “true” lipase gene fragment heterologously in Escherichia coli and obtained proof of hydrolytic activity on Tributyrin, Tween-20, and Olive-oil media. This study resulted in new knowledge on U. lactuca-associated epiphytic bacteria as possible brand-new sources of enzymes such as thiolases and “true” lipases. However, future studies are required to describe the characteristics and important applications of these candidate enzymes.