- Biodiversity loss is of global concern, and is due in part to deforestation and high consumer demand for wood and wood products. The neotropical tree species Cedrela odorata (“Spanish cedar” or “cedro”) is economically valuable for its wood and faces threats of overexploitation. Due to strong similarities in wood features across species, overlapping geographic distributions, and taxonomic uncertainty, other Cedrela species may be intentionally or mistakenly substituted for C. odorata in trade. This pressure is expected to make these species more vulnerable if current logging practices proceed unchecked. This dissertation focuses on the development of genomic resources for C. odorata and five closely allied species in the genus Cedrela. Each chapter describes how the implementation of genomic data can be used to better understand and protect this historically overexploited plant group. Chapter 2 presents a C. odorata leaf transcriptome, chloroplast genome, and a set of probes that can be used to enrich target regions (genes) of the nuclear genome for DNA sequence analysis. I demonstrated that these “target capture” probes efficiently sampled thousands of genes from C. odorata specimens (~ 7,900 genes at 10X depth), the four Cedrela species included (3,000-9,500 genes), closely related and endangered Swietenia mahagoni (Caribbean mahogany; 4,000 genes), and distantly related Guarea guidonia (muskwood; 750 genes) and Trichilia tuberculata (550 genes). This list of genes adds significantly to the available genomic resources for these species (most are currently represented by fewer than 20 genes), and makes a large contribution to genomic resources for the mahogany family (Meliaceae). In Chapter 3, I used the target capture probes to sample the genomes of 168 Cedrela trees representing six co-occurring species, with the goal of determining whether named species can be verified as distinct genetic entities based on robust genomic sampling. Of particular interest was the possibility that C. odorata may contain multiple genetic lineages that are morphologically similar or identical (i.e., cryptic species). I inferred the phylogenetic relationships among C. odorata and closely allied species with nuclear SNPs and chloroplast genomes. I found that C. odorata was clearly represented as two lineages: one in Mesoamerica, and one in South America that included allied species C. fissilis, C. nebulosa, and C. saltensis. I compared seven species delimitation schemes to current taxonomy (i.e., models combining individuals identified as distinct species under the same taxonomic name and/or separating previously grouped individuals). In all cases, species definitions showing simplified taxonomy (fewer species) were better representations of the data than current taxonomy. The best model supported: (i) the separation of Mesoamerican C. odorata sensu stricto and South American C. odorata into distinct taxa, and (ii) combining two previously described species (C. nebulosa and C. saltensis) with South American C. odorata into a single species. If these findings were adopted for Cedrela taxonomy, they would result in reduced taxonomic uncertainty in this genus, and would help streamline documentation of Cedrela in trade. In Chapter 4, I developed and tested a single nucleotide polymorphism (“SNP”) genotyping assay for geographic source validation of C. odorata, a critical need for law enforcement. I demonstrated that array SNPs and resulting genotypes accurately estimate C. odorata geographic origin at the scale of Central vs. South America, and that SNPs provided a median prediction error of 188.7 km from the true origin. This approach has promise for assigning geographic origin of C. odorata wood, and provides useful information for enforcing restrictions on the harvest and trade of C. odorata across its range in the Neotropics. Chapter 5 provides a review the major findings presented in this dissertation, and presents unresolved areas of research that may benefit from these genomic resources. For example, the presented data and methods may provide a starting point for future phylogenetic studies of Cedrela that consider the entire genus. The genomic depth obtained with the probe set should also be adequate to investigate the role of hybridization in the genus Cedrela.