Quantitative differentiation of the inoculated Promicromonospora sp MARS and indigenous microbial flora of rice straw is described using ERIC-PCR during the production of xylanase in non sterile solid state fermentation (NS-SSF) to reduce the cost of enzyme production. Under non-sterile solid state fermentation with rice straw, Promicromonospora sp MARS produced 85.0 IU/g of xylanase. DNA fingerprints of unknown bacterial isolates obtained on BHA + xylan exactly matched with that of Promicromonospora sp MARS. Using PCR based enumeration; population of Promicromonospora sp MARS was 67.5 x 10(5) cfu/g after 48 h which increased to 23 x 10(6) cfu/g after 96 h which coincided with the maximum xylanase activity as compared to 14 x 10(4) cfu/g in control after 96 h. Under submerged fermentation (SmF), after 48 h, Promicromonospora sp MARS produced maximum xylanase (42.2 IU/ml) using rice straw as substrate followed by 19.9 and 20.4 IU/ml when Promicromonospora sp MARS was grown on rice husk and wheat straw, respectively. Optimum pH and temperature of the crude xylanase were 8.0 and 65 degrees C. Crude enzyme was 95% stable for 180 min of incubation at pH 8.0 and was stable at 65 degrees C for 240 min. (C) 2011 Elsevier Ltd. All rights reserved.