Brackish ponds and lagoons located on Polynesian atolls are frequently colonized by thick cyanobacterial mats. The accumulated organic material (OM) is preserved due to prevailing anoxia. The high productivity of these microbial mats is controlled by high nutrient contents in the interstitial waters of the underlying limestone, in accordance with the geothermal endo-upwelling process (Rougerie and Wauthy, 1986, 1993). Observations and micro-analysis carried out on insular phosphate samples, and a comparative study of hydrocarbons extracted from kopara and phosphate, indicate a genetic link between the diagenetic evolution of the trapped OM and the apatite precipitation as follows: growth of thick microbial mats in brackish ponds and closed lagoons, and anoxic preservation of OM; oxydative degradation of these OM, Liberation of PO43- ions to apatite saturation; primary apatite precipitation and phosphatization of the detrital carbonates through substitution of CO3 by PO4; polyphasic enrichment of the phosphate deposit induced by eustatic changes, through primary apatite dissolution and secondary apatite precipitation. This model of phosphogenesis provides explanations that are both qualitative (trapped organic matter and apatite substitution by elements in ratios corresponding to those of deep marine waters) and quantitative (10(6) to 10(8) tons of apatite accumulated on small atolls), lacking in previous models (degradation of guano or volcanic material).