In this study, we studied the environment factors such as plastics and heavy metals affecting the blood and cloacal microbiome of green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) in captivity. By non-metric multidimensional scaling analysis, data has shown that the environment factors (p = 0.02), rather than species differences (p = 0.06), significantly influenced the composition of the cloacal microbiota of green and hawksbill turtles. The cloacal microbiota of both captive green and hawksbill turtles was dominated by several similar dominant phyla at differential abundance. Green turtles' cloacal microbiome was made up of 46% of Proteobacteria, 31% of Bacteroidota, 11% of Campylobacterota and 4% of Firmicutes, while the hawksbill turtles' cloacal microbiome was made up of 33% of Bacteroidota, 18% of Firmicutes, 17% of Proteobacteria, and 2% of Campylobacterota. Water conductivity, salinity, microplastic polymers (polycarbonate, polyethylene terephthalate, polystyrene), and copper are positively associated (p