Paleogenomics research on populations from the tropical Americas has historically been constrained by poor recovery of ancient DNA. While the effects of environmental and thermal conditions on DNA survival have been studied and modeled in ancient samples from temperate contexts, similar methodological research in ancient tropical samples is still lacking. Here we compare DNA preservation in human skeletal remains from two pre-contact tropical contexts in the Americas: the Yaxuná site in the Yucatán peninsula (250-550 CE) (n=6), and the Punta Candelero, Paso del Indio and Tibes sites in Puerto Rico (500-1300 CE) (n=29). We compare the application of two different extraction methods on teeth and, in the Yaxuná samples, petrous portion tissue. All samples were extracted, transformed into libraries, captured for the complete mitochondrial genome and sequenced on the Illumina MiSeq. Preliminary results suggest that endogenous DNA content is lower in the Yaxuna samples than in the Puerto Rican samples irrespective of extraction method. Yields from petrous portions were also unexpectedly low in these samples. There was no statistically significant difference in endogenous DNA recovery from either extraction method across samples from both sites (t(8)=-0.0095, p=0.99). These early findings suggest that DNA survival may be highly dependent on site-specific processes and that efforts to recover ancient genetic material in tropical samples may need to be tailored on a case-by-case basis. We are currently testing these inferences further by exploring the relationship between deposition age and temperature on overall DNA preservation in these samples through a modified model of DNA decay.