AIMS: The influence of bacterial species/strains in agitated culture was investigated on the morphology and structure characteristics of bacterial cellulose. METHODS AND RESULTS: Komagataeibacter nataicola Y19 and Gluconacetobacter entanii ACCC10215 were inoculated in Hestrin–Schramm (HS) medium and subjected to agitated cultivation. Different kinds of BCs were obtained including flocky asterisk‐like BC by G. entanii ACCC10215 and solid sphere‐like BC by K. nataicola Y19. The SEM results showed that the asterisk‐like BC had larger pores than the solid sphere‐like BC. The FT‐IR and X‐ray diffraction results showed the asterisk‐like BC had lower crystallinity (81·43%), higher cellulose Iα mass fraction (79·74%) and smaller crystallite size. CONCLUSIONS: The different species/strains can influence the morphology and structure characteristics of BC in agitated culture. SIGNIFICANCE AND IMPACT OF THE STUDY: We examined the influence of different species/strains on the morphology, macro‐ and microstructure of BCs produced in agitated culture for the first time, which suggest that different BCs with potential applications could be obtained by choosing different species or strains and fermentation method.