A comparative study was carried out on the occurrence, distribution and diversity of microflora in the intertidal mudflats and sandbars at the Nsidung Beach end of the Cross River Estuary, Nigeria between February and April,2009. Samples were analysed within six hours of collection. Identification of microflora was based on standard identification guides and texts. Altogether, 16 microflora taxa belonging to 13 genera and 5 divisions were identified.Over eighty five percent of the microflora was recorded in the mudflats while 14.0% were identified in the sandbars. Diversity indices of 1.69 and 1.59 were obtained for the mudflats and sandbars, respectively. Results of the study arediscussed in relation to the differential nutrient entrapment and retention capacities of the mudflats and sandbars in the estuary
