The productivity and marketable quality of hot pepper (Capsicum annuum var. annuum L.) are low in tropical regions mainly due to virus infections and lack of effective virus management strategies. The absence of effective virus management strategies could be attributed to lack of information on virus vectors and host resistance. Parental (P 1 and P 2 ) and progeny (F 1 , B 1 , B 2 and F 2 ) generations of five hot pepper crosses were grown in Ethiopia at three sites (Bako, Hawasa and Melkasa) to monitor number and species of potential aphid vectors, disease incidence levels with regards to natural infections by Potato virus Y (PVY) and Ethiopian pepper mottle virus (EPMV) complex, and to determine genetic tolerance of the crop to the viruses. Disease incidence was assessed before the flowering stage of the crop plants using visible disease symptoms due to infections by PVY and EPMV. The serological tests revealed presence of symptomless genotypes of the crop to the virus infections. Aphid species potentially transmitting the viruses, such as Acyrthosiphon pisum (Harris), Aphis fabae (Scopoli), and Myzus persicae (Sulzer), were identified from specimens caught by yellow water traps. The highest number of aphids from yellow water traps was recorded at a dense foliage growth stage of the crop at Melkasa. Highly significant variation was observed among generations of the five crosses in response to infections by PVY and EPMV complex. The most susceptible parents had the levels of disease incidences ranging from 80 to 90%, whereas their progenies had only below 30% incidence levels. The most tolerant parent remained symptomless to the natural infections of PVY-and EPMV-complex. Incidence levels in progenies of a cross from the most susceptible and tolerant parents remained below 20%. Based on serological test, the proportion of PVY-positive plants ranged from 0 to 75% and of EPMV-positive plants from 0 to 25%, with 0 to 17% co-infection by the two viruses. Availability of virus sources in the vicinity, efficiency of aphids in vectoring, weather conditions during the growth period, genetic tolerance and the growth stage of the crop affected natural infection by PVY-and EPMV-complex. Exploitation of the genetic potential of introduced elite genotypes and their progenies along with breeding elite local cultivars for resistance Electronic supplementary material The online version of this article (and excluding aphid vectors at young (seedling) stage of the crop plants could be helpful for minimizing losses in yield and quality of hot pepper due to infections by PVY-and EPMV-complex.