This work aims to study amalgavirus diversity in different species of allium collected around the world. Transcriptomic data of 19 Sequence Read Archive runs available at GenBank, as well as RNA-seq data generated from onion tissue from fields in Brazil were used to assemble nine allium cepa amalgavirus 1 (AcAV-1) and nine allium cepa amalgavirus 2 (AcAV-2) genomes from different species of allium worldwide. Sequence demarcation tool analyses of RdRp amino acid sequences revealed identities above 99% within each species, except for an isolate of AcAV-1 from Allium escalonicum from China. This work contributes to the understanding of the genetic diversity of amalgaviruses that infect the genus Allium. Keywords: amalgaviruses; Allium transcriptomic datasets; Allium sp.