Passion fruit, a tropical species cultivated across various nations, faces challenges in expanding its cultivation areas due to several constraints, including total crop losses, caused by the fruit woodiness virus. In Brazil, this condition is attributed to the cowpea aphid-borne mosaic virus (CABMV), and currently, no passion fruit cultivars are resistant to this virus. This research aimed to assess the resistance to CABMV within the third backcross generation (BC3) of passion fruit, employing both phenotypic and genotypic methodologies to identify the most promising families and genotypes. The study utilized a randomized block design and a rating scale to evaluate the manifestation of virus symptoms, facilitating the estimation of the area under the disease progress curve. The 'disease resistance' trait was analyzed using mixed models to estimate variance components through Restricted Maximum Likelihood (REML) and to predict selection gains via Best Unbiased Linear Prediction (BLUP). Twenty-seven microsatellite markers (SSR) were applied to determine the genetic distances among 95 genotypes within the studied population. These SSR markers were effective in differentiating the evaluated groups. Among the top 30 genotypes ranked for CABMV resistance, four genotypes from different families exhibited superior traits, making them suitable candidates for the next backcross generation.