High-throughput RNA sequencing is a powerful tool that allows us to perform gene prediction and analyze tissue-specific overexpression of genes, but also at species level comparisons can be performed, although in a more restricted manner. In the present study complete liver transcriptomes of five tropical bat species were De novo assembled and annotated. Highly expressed genes in the five species were involved in glycolysis and lipid metabolism pathways. Cross-species differential expression analysis was conducted using single copy orthologues shared across the five species. Between 22 and 29 orthologs were upregulated for each species. We detected upregulated expression in Artibeus jamaicensis genes related to fructose metabolism pathway. Such findings can be correlated with A. jamaicensis dietary habits, as it was the unique frugivorous species included. This is the first report of transcriptome assembly by RNA-seq in these species, except for A. jamaicensis and as far as our knowledge is the first cross-species comparisons of transcriptomes and gene expression in tropical bats.