Human-made debris is entering the ocean at alarming rates. These artificial structures are becoming habitats for small marine taxa known as cryptofauna. Cryptofauna are among the most essential reef taxa; however, little is known about these organisms, let alone their fate considering degrading coral reefs and increasing anthropogenic disturbance. The current study explores differences in naturally occurring cryptofauna biodiversity compared to those inhabiting benthic marine debris. To explore this difference, we measured invertebrate diversity from autonomous reef monitoring systems (ARMS) located on patch reefs along the Middle Florida Keys Reef Tract. ARMS were used as a proxy for natural structure to compare to marine debris removed from five reef locations. Plastic debris was the most abundant of all the debris material collected. Wood and concrete were identified as covariates since they are sourced from wooden lobster traps. Taxa diversity varied significantly between ARMS and debris, indicating that each structural unit contained significantly different and diverse communities. The most influential taxa identified included commensal shrimps, hermit crabs, brittle stars, segmented worms, and several families of crabs. Additionally, while functional richness increased with taxa richness for ARMS communities, debris communities showed decreasing functional richness and high functional similarity, suggesting a specialization of debris-specific taxa. Overall, these data assist in better understanding the marine community ecology surrounding anthropogenic marine debris for future debris removal and management practices for comprehensive reef health.