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Background  Tree species in the genus  Cedrela  P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of  Cedrela.  However, few genetic resources exist that enable both species and source identification of  Cedrela  timber products. We developed several ‘omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of  Cedrela  specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus.    Results  We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for  C. odorata,  and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five  Cedrela  species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for  Cedrela  species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the  Cedrela  species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae.    Conclusions  Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for  Cedrela  species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of  Cedrela  and related species in the Meliaceae.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5382-6) contains supplementary material, which is available to authorized users.

Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives