Rabbits are housed on various types of cages including single tier, multi- tier cages etc. The effect of housing system on the floor bacterial load is variable, and its effect on animal production is limited. An attempt has been made to evaluate and compare the floor bacterial load between single-tier and multi-tier caging system in rabbitary. The study was carried out in rabbitary which housed broiler rabbits. The samples were taken in sterile cotton tipped swabs. The floor bacterial load was determined by dilution method where serial dilutions were done with sterile normal saline. An aliquot of 1 ml was taken from dilution and poured in sterile petri plates in triplicate and mixed with liquefied sterilized plate count agar. Following incubation, the bacterial colonies were counted. The bacterial load in the single-tier was comparatively lower than the multi-tier cage even before washing of cages. There was significant difference (P<0.01) in the floor bacterial load before (1.73x1012±0.30) and after water wash (1.35x1011±0.29) and between single (1.50x109±0.30) and multi-tier cages (1.35x1011±0.29). The bacteria up to genes level found using Hi-Media bacterial kit were Staphylococcus aureus, Staphylococcus epidermidis, Flavobacterium sp, Micrococcus sp, Proteus sp, Mannheimia sp, Klebsiella sp, Bordetella sp, Bacillus sp, Actinomyces sp, Cornybacterium sp and Pseudomonas sp. This study concluded that reduced bacterial load found in single tier may be due to good aeration and better handling facilities. In single tier cage the dung and urine gets settled at the floor which facilities easy washing which slows down the bacterial growth.