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Background: Rabies is the oldest fatal zoonotic disease recognised as a neglected tropical disease and is caused by an RNA virus belonging to the genus Lyssavirus, family Rhabdoviridae. Methodology/Principal findings: A deep molecular analysis was conducted on full-length nucleoprotein (N) gene and whole genome sequences of rabies virus from 37 animal brain samples collected between 2012 and 2017 to study the circulation of rabies virus (RABV) variants. The overall aim was to better understand their distribution in Moldova and north-eastern Romania. Both Sanger and high throughput sequencing on Ion Torrent and Illumina platforms were performed. Phylogenetic analysis of the RABV sequences from both Moldova and Romania revealed that all the samples (irrespective of the year of isolation and the species) belonged to a single phylogenetic group: north-eastern Europe (NEE), clustering into three assigned lineages: RO#5, RO#6 and RO#7. Conclusions/Significance: High throughput sequencing of RABV samples from domestic and wild animals was performed for the first time for both countries, providing new insights into virus evolution and epidemiology in this less studied region, expanding our understanding of the disease. Author summary: High throughput sequencing has become a powerful tool for the epidemiological study of the rabies virus. Considering the lack of information from the two geographic areas included in the present research, a collection of samples from 2012 to 2017 from both domestic and wild animals positive for rabies was used to study the circulation of rabies virus variants. The aim was to better understand their distribution in Moldova and north-eastern Romania, two neighbouring countries. Sanger and high throughput sequencing on Ion Torrent and Illumina platforms were used. A single phylogenetic group, revealing the common past evolutionary history of the species, was identified. The phylogenetic group is called north-eastern Europe (NEE) and samples clustered into three assigned lineages RO#5, RO#6 and RO#7. High throughput sequencing on samples from both domestic and wild animals was performed for the first time for both countries, providing new insights into RABV evolution and epidemiology in these areas and expanding our understanding of the disease. [ABSTRACT FROM AUTHOR]