Microbial citric acid has high economic importance and widely used in beverage, food, detergents, cosmetics and pharmaceutical industries. The filamentous fungus Aspergillus niger is a work horse and important cell factory in industry for the production of citric acid. Although in-depth literatures and reviews have been published to explain the biochemistry, biotechnology and genetic engineering study of citric acid production by Aspergillus niger separately but the present review compiled, all the aspects with upto date brief summary of the subject describing microorganisms, substrates and their pre-treatment, screening, fermentation techniques, metabolic engineering, biochemistry, product recovery and numerous biotechnological application of citric acid for simple understanding of microbial citric acid production. The availability of genome sequence of this organism has facilitated numerous studies in gene function, gene regulation, primary and secondary metabolism. An attempt has been also made to address the molecular mechanisms and application of recent advanced techniques such as CRISPR/Cas9 systems in enhancement of citric acid production.