Two isolates were used in this study, Staphylococcus aureus and Escherichia coli were identified according to morphological, physiological and biochemical characteristics. The two bacteria were treated with 100mM of Trehalose to study the effect of this sugar on the preservation of the bacteria from several factors The results showed that Trehalose preserved the S.aureus from dehydration (drying) for one month in room temperature and the Trehalose keep the bacteria more viable in comparison with the control. While no effect was observed in the Trehalose treated E.coli. Trehalose showed it's preservative effect when the bacteria were stored in freeze condition (-20°C) about 4 weeks the percentages of Viable cells of S.aureus treated with Trehalose after 4 weeks was 67% compared with the control 30%, while the results on E.coli was 66% and the control 32%. Results indicated that Trehalose protect the lyophilized bacteria even in the unsuitable environment such as storing in room temperature for four months, the percentage of the viable cells of bacteria treated with Trehalose after 4 months was 27% while the control 2% . Result also showed the protective effects of Trehalose towered the UV irradiation and Electroporated bacteria. While Trehalose had no effect on the protection from antimicrobial substance (antagonism activity), in contrast it showed a considerable effect of protection from antibiotics by increasing the resistance to the antibiotics, result showed that S.aureus treated with trehalose become resist to, Tetracycline, Gentamicin, Erythromycin and Norfloxacin, while the control stilled sensitive to these antibiotics, and no effect were showed on the E.coli in protection from antibiotics.