Invasive Burmese pythons (Python bivittatus) have been reproducing in the Florida Everglades since the 1980s. Introduction of the species was either due to unintentional escapes or intentional releases from snakes obtained through the commercial pet trade. Burmese pythons have caused a precipitous decline in small mammal populations in south Florida. To better understand the invasive population, two mitochondrial loci (mtDNA; 1398 bps) were sequenced on 426 snakes and 22 microsatellites were genotyped on 389 snakes. Concatenated cytochrome b and cytochrome oxidase 1 mtDNA sequences produced six haplotypes with a nucleotide and haplotype diversity of π=0.002 and h=0.097, respectively. The dominant haplotype was highly divergent from the second most frequent haplotype (π =0.0388). The average number of microsatellite alleles and expected heterozygosity were NA = 5.50 and HE = 0.60, respectively. Nuclear Bayesian assignment tests supported two genetically distinct groups and an admixed group. The effective population size was lower than expected for a population of this size (Ne =315.1), but reflective of the overall low genetic diversity. Patterns for genetic diversity between mtDNA and microsatellites were disparate, indicating nuclear introgression of separate mtDNA stocks due to interbreeding among sympatric populations/stocks of P. bivittatus. Alternatively, hybridization between P. molurus and P. bivittatus may have occurred in native or captive populations. The introgression may have occurred in the native range, breeding of disparate stocks in the pet trade, or in the invasive habitat. The invasive Florida Burmese python sequences were similar to the published sequences identified as P. bivittatus and P. molurus, however the nuclear diversity was nearly half of that reported in wild populations sampled within the native range.