Halophilic bacteria are micro-organisms living in hypersaline environments. They have many potential in several fields in life such as industry and agriculture. In this study two isolates were obtained from saline ponds belonging to local company for salts and minerals, Qarun Lake, Fayoum, Egypt, on nutrient agar (NA) medium prepared using pond water. The 16S rRNA sequence analysis showed that the isolate QSLA16 had 80.15% similarity to Uncultured bacterium clone QAMU23 as well as Sphingomonas sp. LE-239 with 79.9% similarity, while the other isolate QSLA17 was similar to Bacillus sp. strain 6 with 74.05%. QSLA16 cell was rod shaped, not spore-forming and gram negative, while QSLA17 cell was sporulated long rod and gram positive. The obtained results of halotolerance assay showed that QSLA16 isolate is a halophilic bacteria as it wasn't able to grow in the absence of salt (0% NaCl). While isolate QSLA17 could grow in the absence of salt (0% NaCl) and therefore considered as halotolerant. The presence of the genes encoding for non-ribosomal lipopeptides (NRPs) was detected in both isolates using PCR technique and these NRPs were determined using high performance liquid chromatography (HPLC). The lipopeptides surfactin and fengycin were produced by both tested isolates, while mycosubtilin was only produced by QSLA17. The antibacterial activities of these salt tolerant isolates against halotolerant clinical pathogens (Staphylococcus aureus, Salmonella typhi and Acinetobacter baumannii) were determined and their potential use in controlling these pathogens as contaminants of sterilized salty whey was examined.