Two genetically distinct retroviral RNAs can be co-packaged if the RNAs are co-expressed in virion producing cells. For Moloney murine leukemia virus (MLV), co-packaged RNAs are not randomly selected from among all packaging-competent RNAs, but instead primarily associate as homodimers. Here, we tested the hypothesis that the distance between proviral templates might hinder RNA heterodimerization, thus generating the observed preferential homodimerization of co-expressed MLV RNAs. To do this, two genetically distinct RNAs were co-expressed from a single locus and the proportions of hetero- and homodimeric virion RNAs were determined. Unlike RNAs transcribed from two different templates, RNAs transcribed from a single locus dimerized at random. Additionally, in vitro transcription experiments suggested that MLV RNA dimerization can occur more efficiently for longer RNAs during transcription than post-synthesis. Together, these findings show that MLV RNA dimer-partner selection likely occurs either co-transcriptionally or within a pool of transcripts near the proviral template.