Summary Breast milk has recently been recognized as source of commensal and potential probiotic bacteria. The present study investigated whether viable strains of gut‐associated obligate anaerobes are shared between the maternal and neonatal gut ecosystem via breastfeeding. Maternal faeces, breast milk and corresponding neonatal faeces collected from seven mothers‐neonate pairs at three neonatal sampling points were analyzed by culture‐independent (pyrosequencing) and culture‐dependent methods (16 S rRNA gene sequencing, pulsed field gel electrophoresis, random amplified polymorphic DNA and repetitive extragenic palindromic polymerase chain reaction. Pyrosequencing allowed identifying gut‐associated obligate anaerobic genera, like B ifidobacterium , B acteroides , P arabacteroides and members of the C lostridia ( B lautia , C lostridium , C ollinsella and V eillonella ) shared between maternal faeces, breast milk and neonatal faeces. Using culture, a viable strain of B ifidobacterium breve was shown to be shared between all three ecosystems within one mother–neonate pair. Furthermore, pyrosequencing revealed that several butyrate‐producing members of the C lostridia ( C oprococcus , F aecalibacterium , R oseburia and S ubdoligranulum ) were shared between maternal faeces and breast milk. This study shows that (viable) obligate gut‐associated anaerobes may be vertically transferred from mother to neonate via breastfeeding. Thus, our data support the recently suggested hypothesis of a novel way of mother–neonate communication, in which maternal gut bacteria reach breast milk via an entero‐mammary pathway to influence neonatal gut colonization and maturation of the immune system.