In 2017, USDA-FSIS compliance guidelines for Siluriformes, implemented the testing of generic Escherichia coli to ensure product wholesomeness and safety. The BAP standards for processed fish call for rejection of sample if from n= 5 subsamples, 3 or more subsamples exceed 4 MPN per gram or any subsample exceed 40 MPN per gram. Others have placed a limit of 1 CFU/g. E. coli and other indicator organisms in catfish, liquid and environment of processing facilities were assessed by season and time of day. Environmental, fish, and liquid samples were collected in 3MTM Swab-Sampler (with 10 ml of Buffered Peptone Water) and Whirl-pak® sterilized stomacher bags respectively from two different catfish processing plants. (site) located in the state of Mississippi, USA. Replications were defined by the number of visits. Each two visits represented a season and for each visit, 25 samples were collected. All samples were plated on the following corresponding media: aerobic plate (APC), psychotropic plate (PPC), and indicator organisms: generic E. coli, total coliforms (TCC), and Enterobacter following FDA-BAM and AOAC methods. Escherichia coli counts were similar (P ≤ 0.05) for all sampling points with slightly higher incidence in the late Summer than the other seasons. Within the types of sampling, liquid and fish part sample had higher counts than (p≤0.05) environmental samples. Liquid samples consisting of truck water (5.3 log CFU/ml) and chilled water (5.1 log CFU/ml) resulted in higher counts than (p≤0.05) offal water and injector solution (4.4,4.7 log CFU/g, respectively). It is possible that the presence of indicator organisms evaluated varies according to the sampling season, considering that such microorganisms have been found to have a relationship with pathogens, E. coli could be part of the natural microflora of the catfish ponds, thus not a good fecal indicator