These experiments were conducted to study the response of some Egyptian cotton, Giza 96 (extra-long stable) and Giza Giza 96 (extra-long stable)varieties and its yield characteristic, lint percentage, fiber and yarn properties when using bio-fertilizers such as vermicompost, Bacteria  bacteria inoculums (Bacillus polymxa, Bacillus megaterium and Bacillus circulans) and algae extract under different growing area, Sakha region (clay soil) and El-Nubaria region (calcareous soil).Concerning the effect of different treatments application on soil properties, thisresults showed a significantly increaseof soil organic matter, pHit was relatively insignificantly decreased and the vermicompost treatments had positive effects on the levels of N, P and K. available. As soil biological count of Bacteria, Fungi, Actinomycetes and Carbon dioxide evolution rate it showed a significant increase. The content of cotton plant leaves of chlorophyll A, B, Carotenoids and Total phenols was significantly improved under different fertilizer treatments compared to the control.The treatment with (vermicompost fertilizer + bacterial inoculation + 50% of mineral fertilizer recommended dose + algae extract) proved its superiority over the rest of the treatments, especially in the seed cotton yield, and lint percentage, which increased at 1.41 kentar per feddan and 0.63(lint %) compared to the two control treatments. Data of cotton yield characteristics, fiber and yarn properties were recorded significantly different due to cultivated in different regions.The difference among studied varieties may be due to the growth habit and response of each one to environmental conditions, which controlled by genetic factors and efficient utilization of inputs and natural resources.