Microplastics are persistent environmental contaminants, and fungi associated with mangrove roots may offer a source of isolates for studying interactions with polymeric materials. This exploratory study profiled fungal DNA in a single pooled sample of Rhizophora apiculata roots using ITS amplicon sequencing and examined the FTIR spectra of polycaprolactone (PCL) samples following exposure to five cultured fungal isolates, designated fungal isolates S2–S6. Amplicon sequencing detected 48 fungal taxa, predominantly assigned to Ascomycota, with Aspergillus as the most abundant genus. The diversity indices suggested moderate diversity and relatively low dominance within the pooled sample. FTIR analysis revealed differences in PCL associated spectral features following exposure to the isolates, while principal component analysis (PCA) showed preliminary spectral differentiation among the analyzed samples. These observations indicate differences in the chemical or surface associated characteristics of the tested PCL samples; they do not demonstrate polymer mass loss, depolymerization, assimilation, or mineralization. The sequencing results represent fungal DNA detected in one pooled biological sample and do not establish the viability or endophytic status of the detected taxa. A correspondence between the cultured isolates and the detected amplicon sequence variants was not established. Quantitative mass-loss measurements, molecular weight and degradation product analyses, and experiments with appropriate controls and biological replication are needed to determine the nature and cause of the observed PCL associated spectral changes.