Resilient coral communities have settled on artificial structures (concrete walls and riprap) within the basins of Port of Miami, Florida. To investigate the molecular basis of coral resilience to the stressful environmental conditions usually associated with urban locations, we generated whole transcriptome expression profiles for 31 Pseudodiploria strigosa colonies from these locations and a nearby offshore reef. Differential expression analysis between urban corals and offshore corals revealed a suite of molecular mechanisms allowing urban corals to withstand the poor-quality waters. P. strigosa corals from the urban locations have higher expression of 1) transcripts that encode pattern recognition receptors allowing these corals to sense and detect food particles and pathogenic invaders, 2) digestive and degrading enzymes enabling urban corals to carry out heterotrophic feeding and to digest potential pathogens, 3) transcripts related to innate immunity, defense and cellular detoxification protecting pathogenic organisms and water pollution. Our data shows that the studied urban corals are well equipped to defend themselves against frequent high bacterial and plankton concentrations and that they might rely on heterotrophic feeding for supplemental nutrition to fight off the stressful conditions. In addition, we have found that urban corals exhibit higher expression of proteins that are components of coral oocytes (vitellogenins and lipovitellins), suggesting that these corals might be in better health to dedicate more resources towards reproductive processes. We have also determined the symbiont types hosted by P. strigosa using reads that mapped to the SSU rRNA symbiont genes. This analysis revealed that P. strigosa colonies from the urban sites predominantly host symbionts from the genus Durusdinium. In contrast, the offshore colonies of this coral species exclusively host symbionts from the genus Breviolum. This result corroborates the previous finding on the inshore corals relying on Durusdinium symbionts to survive in urbanized waters. While transcriptomics plasticity revealed phenotypic variability within the Miami P. strigosa population, we hope that this study will open opportunities for developing genetic markers to determine if the differences between urban and offshore corals are based on their genetics. Genotyping the urban coral communities will hopefully foster further research on using these coral genotypes in restoration activities.