This study investigated differences in Symbiodinium diversity in the scleractinian coral species Agaricia lamarcki between shallow (20–25 m) and mesophotic (50–70 m) depths in the Northern Caribbean. Corals were sampled in each of four shallow sites (20–25 m; n = 18) and three mesophotic sites (50–70 m; n = 18) from Mona Island (Puerto Rico) and the US Virgin Islands during a mesophotic exploratory cruise and from the La Parguera shelf edge, off Southwestern Puerto Rico. Symbiodinium diversity was assessed using internal transcribed spacer 2 sequences clustered into operational taxonomic units (OTUs). Clustering resulted in eight clade C OTUs and one clade D OTU. Of these, there were three common Symbiodinium OTUs consisting of C3 and D1a.N14 in shallow reefs and C11.N4 in mesophotic reefs. Statistical tests (permutational multivariate analysis of variance and analysis of similarity) showed significant differences between clade C Symbiodinium OTUs in A. lamarcki colonies located at shallow and mesophotic depths, indicating symbiont zonation. Symbiodinium diversity in A. lamarcki from the Northern Caribbean is comparable to previous reports in the Southern Caribbean for this species. This is the first report of the thermal tolerant species Symbiodinium trenchii (D1a) in A. lamarcki.