Viruses that replicate by reverse transcription of RNA into DNA fall into two distinct viral families. These are retroviruses such as human immunodeficiency virus (HIV) that carry two copies of a single-stranded, linear RNA genome; and hepadnaviruses such as hepatitis B virus (HBV) that comprise a partially double-stranded, circular DNA genome. To date, studies of bat genomes and transcriptomes have yielded a diverse variety of sequences representing multiple retroviral genera; yet the goal of isolating replication competent exogenous retroviruses from bats has remained elusive. Nevertheless, the abundant sequences present in the genomes of both major groups of bats represent a tantalizing fossil record of past retroviral infections, and imply a strong likelihood that bat retroviruses will eventually be isolated. Furthermore, bats are natural reservoirs of several HBV-like viruses, implicating them as a possible ancestral source and natural reservoir of HBV. Phylogenetic studies comparing retroviral sequences in bats to extant retroviruses in other species have revealed a diverse set of gammaretroviruses and betaretroviruses. This finding suggests that bats may have harbored early members of the mammalian gammaretrovirus genus, which includes the contemporary animal pathogen koala retrovirus (KoRV), which is associated with leukemia and lymphoma in koalas and consequent population decline. Endogenous betaretroviruses in bats cluster into eight distinct subgroups and include some with intact viral genomes that could potentially encode infectious viral particles. These studies suggest that cross-species transmission of gammaretroviruses and betaretroviruses from bats to other mammals has already occurred and may occur again. The practice of hunting bats as a source of bushmeat would create the ideal conditions for potential spillover of retroviruses and hepadnaviruses from bats to humans. Given that both retroviruses and hepadnaviruses are known to cause serious human diseases, it remains an important task to search for and investigate the presence of reverse transcribing viruses in bats.