Disease is contributing to the decline of coral reefs globally, but the cause and pathogenesis of most coral diseases are poorly understood. Using Gorgonia ventalina and G. flabellum as a model for coral disease diagnosis, we histologically and microbiologically examined 45 biopsies of lesions resembling Gorgonia multifocal purple spots (MFPS) with the aim of forming a comprehensive case definition based on gross and microscopic morphologic descriptions and associated etiologies. Macroscopically, all lesions were small circular areas of purple pigmentation. Gross morphologies included pigmentation only (4/45, 9%), or pigmentation with branchlet expansion and fusion (19/45, 22%), sessile masses (17/45, 38%), or hard nodules (5/45, 9%). Histological morphologic diagnoses included amoebocyte encapsulation (9/45, 20%), coenenchymal amoebocytosis (6/45, 13%), melanin (17/45, 38%), and gorgonin deposition (13/45, 29%). Sixty-four percent of instances of fungi and 86% of labyrinthulomycetes were localized to grossly normal portions of the biopsy, whereas barnacles were only within lesions, and 87% of instances of algae and 82% of cyanobacteria were within lesioned area of the biopsy. Penicillium (n = 12) was the predominant genus of fungi isolated from biopsies. Barnacles were identified as Conopea sp. using molecular techniques. The pathology and etiology underlying MFPS lesions are diverse, consistent with a highly nonspecific lesion pattern rather than a specific disease. This study demonstrates the importance of microscopic examination of tissues for accurate classification of coral diseases and lesion patterns.