There is a huge demand for coffee in the Philippines, but local supply has a long way to go at catching up. One way to aid local farmers is to develop coffee varieties with combined desirable traits including natural resistance against various diseases and insect pests. This can increase product output and reduce costs on chemical control that can, in turn, potentially increase their profits. This paper reviews and gives an overview of the genetic research on coffee toward improving plant defense. The most prominent diseases and pests plaguing plantations worldwide are noted. From studies using classical tools such as genetic marker analysis to recent ones using newer tools such as genomics and bioinformatics, global accomplishments are discussed alongside accomplishments in the Philippines. Inferences are also made from data collated from these studies. Overall, this review paper aims to assess the status of coffee research and identify gaps as well as prospects and needs for further investigation.