Cold seeps have recently been discovered in the Nile deep-sea fan (Eastern Mediterranean), and data regarding associated fauna are still scarce. In this study, two bivalve species associated with carbonate crusts and reduced sediment are identified based on sequence analysis of their 18S and 28S rRNA-encoding genes, and associated bacterial symbioses are investigated using 16S rRNA gene sequencing and microscopy-based approaches. The specimens are closely related to Myrtea spinifera and Thyasira flexuosa, two species previously documented at various depths from other regions but not yet reported from the Eastern Mediterranean. Both species harbour abundant gammaproteobacterial endosymbionts in specialized gill epithelial cells. The Myrtea-associated bacterium is closely related to lucinid symbionts from both deep-sea and coastal species, whereas the Thyasira-associated bacterium is closely related to the symbiont of a T. flexuosa from coastal waters off the U.K. An epsilonproteobacterial sequence has also been identified in Thyasira which could correspond to a helicoid-shaped morphotype observed by electron microscopy, but this was not confirmed using fluorescent in situ hybridization. Virus-like particles were observed within some symbionts in Thyasira, mostly in bacteriocytes localized close to the ciliated zone of the gill filament. Overall, results indicate that very close relatives of shallow species M. spinifera and T. flexuosa occur at cold seeps in the Eastern Mediterranean and harbour chemoautotrophic symbioses similar to those found in their coastal relatives.