Objective of this study was to evaluate the effect of supplementation of growing rabbits’ diet with 5% spirulina (Arthrospira platensis) and/or 3% (Thymus vulgaris L.), on composition and amount of rabbits caecal microbiota. After weaning, rabbits were randomly sorted to 4 groups (n ¼ 42/group). The control group received a pellet without any supplementation, in treated groups the dietary supplementation was provided until 77 days of age. On 49, 63 and 77 days of age, six healthy animals/group were randomly selected and slaughtered. From the caecal content the amount of total bacteria, Bacteroides, Clostridium leptum and Clostridium coccoides were determined by quantitative polymerase chain reaction (qPCR), with the aid of bacterial ribosome coding DNA. The copy number of total bacteria, C. leptum, C. coccoides and Bacteroides varied between 2.75 1012 to 2.24 1013, 5.25 1011 to 1.82 1012, 2.5 1010 to 6.91 1011 and 5.89 1010 to 1.10 1012, respectively. The amount of investigated bacteria represented 0.6%- 13.4% of the total bacteria. The use of spirulina and/or thyme supplements influenced the amount of the copy number of each bacteria examined between 49 and 77 days of age. Their effect on the total bacteria number was temporary. Spirulina resulted in more Bacteroides on day 63 but significantly lower amount of Clostridia at 63 and at 77 days of age. The antimicrobial effect of thyme on the absolute Clostridia number was temporary, prevailing on day 63. Thyme resulted in significantly decreasing percentage ratio (within total bacteria) of C. leptum and C. coccoides by 77 days of age.