This thesis is an investigation of the molecular biodiversity of bats in the neotropical regions of Central and South America employing DNA barcoding using the cytochrome 'c' oxidase subunit 1 gene, an analysis of molecular evolution, comparisons between patterns of diversity in maternally and paternally inherited genetic regions, and morphological and acoustic assessments of potential cryptic species. In chapter 1, DNA barcoding suggests that as much as 40% of the taxonomic richness of this group may be undescribed and also indicates a high level of intraspecific molecular variability. Molecular diversity is investigated in chapter 2 by comparing bats to rodents and passerine birds using measures of nucleotide and amino acid diversity, selection and relative rate analysis. In all tests of nucleotide diversity, bats are highly variable and more similar to rodents than passerines. All three groups experience extreme purifying selection though it is significantly reduced in birds. While bats and rodents experience the same selection pressure, the permitted amino acid replacements are more structurally dramatic in rodents which also show evidence of historical selective sweeps in 30% of species pairs - a pattern not detected in either bats or passerines. In chapter 3, potential taxonomic diversity is explored by using a paternally inherited intron region to test for gene flow in seven groups where DNA barcoding suggests potential cryptic species. In four of the tested species, distinct maternal groups are supported by fixed characters in the paternally inherited region indicating a complete cessation of gene flow and supporting the existence of species complexes. In chapter 4, one of these complexes, 'Pteronotus parnellii ', is investigated using both morphology and acoustic techniques. Significant morphological variation and diverse phonic groups exist supporting the genetic patterns and further confirming the existence of cryptic species. The pattern of phonic variation suggests that acoustic patterns are diverging by drift or through social selection rather than to facilitate resource partitioning. Encompassing DNA sequences derived from nearly 17,000 specimens, including >9,000 representing 161 species of bat, this is the largest survey of molecular biodiversity of bats ever conducted.