Mucoepidermoid carcinoma (MEC) is one of the most common salivary gland cancers, comprising 30-40% of all salivary malignancies. Importantly, a common family of translocations, CRTC(1/3)-MAML2 rearrangements, have been well established as highly recurrent genomic events driving disease progression in half of all cases. Until recently, however, the molecular basis of this disease beyond these rearrangements was largely unknown. While understanding the molecular etiology of MEC tumors is complicated by significant intra- and inter-tumor heterogeneity, several recent studies have made significant strides characterizing this disease. This review focuses on synthesizing the data from the current literature to further elucidate the role of additional somatic genomic alterations, including TERT translocations, chr9p21.3 and 8q24.3 copy number alterations, and NOTCH pathway mutations, that drive the molecular biology of this disease. These discoveries have been crucial to understanding MEC molecular etiology.