Xanthomonas campestris pv. mori causes bacterial leaf spot (BLS) of mulberry (Morus spp.) worldwide. Twenty mulberry lines with contrasting response to BLS showed significant (p < 0.01) variation between resistant and susceptible groups for stomata frequency (SF), trichome density (TD), total soluble sugar (TSS) and polyphenol (PP) content, while non-significant for chlorophyll content. Heritability (broad-sense) estimates obtained from the variance component analysis were high (≥0.72) for these traits. The disease severity index values of the lines were significantly negatively correlated with TD (r = −0.66; p < 0.01), TSS (r = −0.73; p < 0.01) and PP (r = −0.61; p < 0.01), while positively correlated with SF (r = 0.65; p < 0.01). The cluster analysis was based on highly significant four variables and DSI values, and classified the lines into two major clusters. The resistant lines that come under cluster-I had high TD, TSS and PP, while those in susceptible category had high SF in cluster-II. These findings suggest that direct selection for SF, TD, TSS and PP will be effective for development of host resistance against BLS in mulberry.