Bacterial biofilms are known to affect operational performance of membrane filtration, but little knowledge is available concerning the mechanisms and factors involved in their formation. The present work aimed to characterize pioneer colonizer bacteria involved in biofilm formation on filtration membranes during dairy fluids treatments. In this context, a laboratory-scale crossflow filtration model system has been designed consisting in an assembly of 4 parallel filtration units (CF042, Sterlitech) each equipped with a UF membrane of 42 cm² flat polyethersulfone (PES) sheet with a molecular weight cut-off of 10 kDa. The dairy fluids studied were raw and pasteurized skim milk, unpasteurized cheese whey and pasteurized cheese whey from the same batch of raw milk. UF separations were performed in full-recycle mode at 40°C for 5 h. After UF operations, membranes were collected before and after cleaning procedure (pH 10.5, 150 ppm of free chlorine, 45°C, 30 min.) for DNA extraction (phenol-chloroform extraction). All experiments were performed in duplicate. A high correlation (R² = 0.93) was found between DNA recovery on UF membranes after water flush (before cleaning) and the initial microbial load of the fluid; whey pasteurization reduced significantly the amount of DNA recovered on the membrane coupons before cleaning (P < 0.05). After cleaning, genomic DNA was still detectable on membranes coupons. Indeed, preliminary results showed that even with a higher initial microbial load, unpasteurized cheese whey left the lowest amount of DNA (2.76 ng DNA/cm²) compared with both milk samples (3.86 and 4.71 ng DNA/cm²). Sequencing of the extracted metagenomic DNA is currently in preparation (MiSeq, Illumina) to establish the portrait of the rising bacterial ecosystem located on PES membranes. Our results will translate into designing processing conditions for a better control of biofouling and consequently process efficiency.