<p>This study was conducted in situ to phenotypically characterise 28 accessions of calla lily (<i>Zantedeschia spp</i>.) sampled in 19 locations in Kenya and Rwanda. Ten plants per accession were sampled from each location for data collection on 15 quantitative and 24 qualitative traits. Data was subjected to descriptive statistics, multivariate analysis, as well as cluster analysis using Microsoft Excel, SAS 9.4 and JMP Pro 18, respectively. The accessions displayed differences in qualitative traits such as spathe colour and the presence of spots on the leaf blade. However, these variations did not result in a higher Shannon–Wiener diversity index. All the accessions showed variations in the quantitative traits and there was a strong positive correlation among most of the traits. The principal component analysis placed the accessions in 13 significant axes, while the discriminant analysis of quantitative traits clustered the accessions in 9 canonical functions. Notably, plotting of the first two principal components and canonical functions effectively clustered the six accessions with green spathe. The cluster analysis using qualitative traits grouped calla lily accessions into three clusters. When both quantitative and qualitative data were combined, the analysis again formed three clusters, with one clearly defined group consisting of six green-spathed accessions. These findings suggest that morphological traits used in this study were sufficient to identify a distinct group but were limited in distinguishing the remaining accessions. Hence, this study recommends using advanced technologies such as biochemical and molecular techniques for the characterisation of Kenyan and Rwandan calla lily accessions.</p>