Alectra vogelii has been the major constraint known to attack leguminous species especially to cowpea production. Identification of genetic variation of A.vogelii is a pre-requisite for developing improved cowpea varieties. Hence, the objective of the experiment was the identification of phylogenetically differences and differential responses of A. vogelii found in cowpeas, bambara groundnuts and sunflower from selected parts of Malawi and Tanzania.The first objective, total of 240 SSRs (Rice bean, S. gesnerioides and S. hermothica markers), ISSRs, cpDNA and mtDNA primers used to determine the genetic variability of A.vogelii. The PCR master mix reaction volume of 25μl, containing 2.5μl of 10X PCR buffer, sterile distilled water, 1μM of each primer, 1mM of each dNTPs, 0.5U/μl of TaqDNA polymerase and 50 ng DNA. PCR and gel electrophoresis ran. High coefficients of genetic similarity were revelled among A.vogelii variants. The 29 A.vogelii isolates examined was clustered into six main groups. The identified genetic variability of the A.vogelii will help in effective breeding of sunflower, bambara groundnuts and groundnuts. Second objective, the 23 isolates of A. vogelii was infested to 11 cowpea varieties/lines (Vuli 1, Vuli 2, Fahari, Tumaini, IT99K-573-1, IT99K-7-21-2-2-1, IT00K-1263, IT99K-1122, IT82K-16, B301, Bunda 1, and TZA 263), made a total of 492 pots. Approximately 500 A. vogelii seeds were infested in the prepared pots, 3 seeds of cowpea were sown approximately 5cm deep. The number of emerged A. vogelii plants was counted. The results show that, there is high variability in cowpeas depending on number of the parasite emergence and time of emergence. Third objective, a total of 21 A.vogelii isolate was infested to Bambara groundnuts, peanuts and soyabeans, which made the total of 126 pots. The plants were watered after every 3 days. The number of emerged A. vogelii plants was counted at 6th, 8th, 10th and 12thweeks after pot infestation. Both A.vogelii isolates from Tanzania and Malawi showed late emergence and were more reactive on bambara groundnuts than on soyabean and groundnuts.