The evolution of bacteria is driven by random genetic mutations and horizontal gene transfer (HGT) of genetic material from other bacteria. HGT can occur via transformation, transduction, and conjugation. Here, we present a potential new mechanism of HGT which occurs in a syntrophic Clostridium coculture. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, the two organisms undergo heterologous cell fusion, which includes fusion of the peptidoglycan cell walls and membranes. Heterologous cell fusion facilitated a large-scale exchange of cytoplasmic protein and RNA between the two organisms, leading to the formation of hybrid bacterial cells containing cytoplasmic material of the two parent organisms. Here we present new evidence that cell fusion events also facilitate the exchange of plasmid DNA between the two organisms of the syntrophic coculture. Through the use of a selective subculturing process, we successfully isolated wild-type C. acetobutylicum clones which have acquired a portion of the plasmid DNA, containing the antibiotic resistance marker, from a recombinant strain of C. ljungdahlii. Fusion events led to formation of persistent aberrant hybrid cells with distinct morphogenetic characteristics. Furthermore, our data support the concept of a novel, interspecies, mechanism of acquiring antibiotic resistance. Since neither organism contains any known conjugation machinery or mechanism, these findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.