Camels (Camelus dromedarius) are the most valuable desert animals in Egypt, survive and health of camel calves is the main aim of breeders.The studies on microbial conjunctivitis of newborn camel calves after parturition and their relation to vaginal microbes are rare and important to avoid blindness. Fifty pregnant she-camels were noticed till parturition. Vaginal swabs of mother camels and conjunctival swabs of their newborns were taken after parturition. From microbiological examination, several microbes could be isolated as follow; E. coli, Pseudomonas aeroginosa, Enterobacter sp., Proteus sp., Staphylococcus epidermidis, Streptococcus sp., Corynebacterium sp., Bacillus sp. and Candida sp. From vaginal and conjunctival swabs, E. coli was the predominant isolates. Molecular identification by PCR was done on selected 3 E. coli isolates from conjunctivitis swabs of newborns camel calves. Antimicrobial resistance was found in E. coli isolates to common used antibiotics. The mean results of antibiotic sensitivity were cleared. The E. coli isolates showed high resistance against 4 of tested 6 antibiotics with percentage of 66.67% which were Amoxicillin, Ampicillin, Tetracycline and Trimethoprim -Sulfamethoxazole. On the other hand, they were sensitive to only Azthromycin with percentage of 16.66% and intermediate to Streptomycin (16.67 %).The sensitivity to natural anti-microbial activity of marine microalgae (Nannocloropsis oculata) was investigated as trial to overcome antimicrobial resistance. Further studies are recommended to develop new veterinary pharmaceutical agents.