The scope of this study was the investigation of foaming due to the overgrowth of the filamentous microorganisms M. parvicella and G. amarae. In order to overcome the difficulties arising from the implementation of the traditional technique of Pitt and Jenkins, a molecular counting technique was developed with the use of the Fluorescent In Situ Hybridization (FISH). As was expected the average counts of the filaments identified by the two methods were statistically different since FISH identifies only the viable bacteria while the Pitt and Jenkins technique accounts for the total of the gram positive bacteria. Furthermore, the average counts as identified by FISH weren’t statistically different compared to those counted by means of the LIVE/DEAD technique that identifies only the live bacteria. Therefore, FISH within the scope of this study was used to determine the viable microorganisms. After FISH was developed it was used to investigate the overgrowth of the filaments M. parvicella and G. amarae at the various processes of three WasteWater Treatment Plants (WWTPs) (of the cities of Chalkida, Volos and Psyttalia).The WWTPs were selected based on the severity and persistence of filamentous foaming events in their activated sludge systems. The scope was to test the hypothesis that filaments’ recirculation, by means of the underflows from the solids treatment line, seed the activated sludge system. Furthermore, the WWTPs were selected based on the fact that their solids treatment process included anaerobic digestion for the stabilization of the waste activated sludge in order to calculate the filaments destruction there. The results indicated a seasonal variation of the filamentous bacteria and in specific, the overgrowth of Μ. parvicella and G. amarae during winter and summer months respectively. Also, the mass balances for the filaments showed that they could survive in the anaerobic digestion systems of the WWTPs (destruction rates ranged within 36,2 - 77,6%) and that the underflows from the thickening and dewatering processes seed the activated sludge system with viable Μ. parvicella and G. amarae at percentages equal to 0,4% - 27,1% of the total filament mass in the secondary treatment. In order to investigate the viability of G. amarae and M. Parvicella in anaerobic digestion, a laboratory scale study was conducted that involved the operation of four lab-scale anaerobic digestion systems, two single - stage and two dual - stage, operating in the mesophilic (35oC) and thermophilic (55oC) temperature ranges. All systems were operated at four different detention times of 20, 16, 13 and 10 days. According to FISH counts of M. Parvicella and G. amarae, it appears that thermophilic conditions resulted in a higher destruction of the filamentous bacteria that averaged from 77,8% to 97,1% and 79,1% - 97,4% respectively, compared to the mesophilic systems that exhibited destruction rates within the range of 51,1% - 76,9% and 59,6% - 69,6%. Destruction rate was proportional to the detention time for all digestion systems. It should be underlined, however, that although anaerobic conditions induced a higher destruction of the filamentous foaming bacteria, they did not improve the sludge foaming characteristics significantly. ..