The human gut microbiota plays an important role in human health and might also be implicated in kidney disease. The interest in butyrate producing bacteria has recently increased and is a poorly understood faecal condition in chronic kidney disease (CKD). Therefore, we evaluated differences of the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii in the faeces of Chinese patients with CKD. A case-control study was carried out for 65 CKD patients and 20 healthy controls. Differences were quantitatively validated using quantitative real-time polymerase chain reaction (qPCR). Spearman rank correlation was used to analyse the correlation between gut microbiota and clinical variables. Roseburia spp. and F. prausnitzii were significantly different in CKD patients and controls (p = 0.001; p = 0.025, respectively) and reduced more markedly in end stage renal disease (p = 0.000; p = 0.003, respectively) and microinflammation (p = 0.004; p = 0.001, respectively). Roseburia spp. and F. prausnitzii were negatively associated with C-reactive protein in plasma (r = -0.493, p = 0.00; r = -0.528, p = 0.000; respectively) and Cystatin C (r = -0.321, p = 0.006; r = -0.445, p = 0.000; respectively). They were positively associated with eGFR (r = 0.347, p = 0.002; r = 0.416, p = 0.000; respectively). The negative correlation between Roseburia spp., F. prausnitzii and CRP and renal function suggested that the depletion of butyrate producing bacteria may contribute to CKD-associated inflammation and CKD progression. Roseburia spp. and F. prausnitzii may thus serve as 'microbiomarkers'.