Congenital amusia is a neurodevelopmental disorder of music processing, which includes impaired pitch memory, associated to abnormalities in the right fronto-temporal network. Previous research has shown that tonal structures (as defined by the Western musical system) improve short-term memory performance for short tone sequences (in comparison to atonal versions) in non-musician listeners, but the tonal structures only benefited response times in amusic individuals. We here tested the potential benefit of tonal structures for short-term memory with more complex musical material. Congenital amusics and their matched nonmusician controls were required to indicate whether two excerpts were the same or different. Results confirmed impaired performance of amusic individuals in this short-term memory task. However, most importantly, both groups of participants showed better memory performance for tonal material than for atonal material. These results revealed that even amusics' impaired short-term memory for pitch shows classical characteristics of short-term memory, that is the mnemonic benefit of structure in the to-be-memorized material. The findings show that amusic individuals have acquired some implicit knowledge of regularities of their culture, allowing for implicit processing of tonal structures, which benefits to memory even for complex material.