Foraminifera unicellular protozoan whose high level taxonomical studies are based on shell mineralogy can be categorized into four groups as taxa with organic shell, agglutinated taxa, calcareous perforate taxa and calcareous imperforate and habituating in marine environments such as coral reef and mangrove. For the present study benthic foraminifer fauna has been collected in the Van veen grab sampler in the Sosistris Bay and North Bay of Port Blair India. These reef dwelling foraminifera host algal symbionts have substantial promise as indicators of coral reef vitality because physiological analogies between coral and foraminifera require similar environmental conditions. To study the Shell abnormalities such as stunted foraminifera shells, abnormal wall structures and shell deformation, mineralogical projection, micro borings, pitted surface, calcification anomalies, dissolution and shell deformation in foraminifera the light microscopic SEM and EDAX studies are carried out. The basic finding of the study reveals that shell abnormalities are common in foraminifers’ species. More than three morphological anomalous found in the peneroplis genus .The high frequency of morphological anomalies of foraminifera indicates that the abnormities are associated with induction of heavy metals such as Zn, Fe, Pb and Zn into crystalline frame work of foraminifera shell. Heavy metal contamination of the environmental conditions including geochemical habitat or human influence. Pervasiveness of such features indicates that these foraminifera and its impact in marine environment. The main pollutants are chemical like heavy metals, organic sewage, nutrients, and hydrocarbons and physical like thermal, and oil.