With the increase of seaweed farming activities, epiphytic filamentous algae (EFA) disease has appeared in many regions of Madagascar. This infestation has dramatic consequences for local farmers as it alters drastically farmed algal growth and has caused farming activity to collapse in many places. The present study characterizes the structure and ultrastructure of the stages observed in the life cycle of Polysiphonia sp. and gives the results of a monitoring of 18 months made in three Kappaphycus alvarezii farming sites in the southwest of Madagascar. Transmission electron microscopy (TEM) was used to analyze the ultrastructure of the cortex in infested K. alvarezii. Five stages have been observed in the life cycle of Polysiphonia sp.: the infesting stage that is a small dark spot observed at the surface of K. alvarezii, the male gametophyte, the female gametophyte, the tetrasporocysts, and the undifferentiated stage where individuals show normal thalli without sexual differentiation. EFA infestation was never recorded in Sarodrano, but often in the two other monitored villages (Lambohara, Tampolove). Prevalence of infestation varied from 40 to 100 % and the rates of infestation from 42 to 78 epiphytes cm−2. Prevalence of infestation showed significant seasonal variation and a between-sites variation; the rates of infestation were not significantly different between sites and did not vary with the period. The ways of infestation between K. alvarezii individuals in an infested field and from infested to healthy fields are discussed at the light of the present results.