The Andes are the domestication center of many important and minor crops. The list of Andean crops with available high-quality genome assemblies is biased towards crops with worldwide distribution, neglecting those cultivated locally that have significant agricultural and cultural value. After potato, olluco (Ullucus tuberosus, Basellaceae; 2n = 2x = 24) is the second most cultivated tuber crop in the Central Andes. Here we report phased diploid genome assemblies at a chromosomal scale. We assembled the haplomes (utub_hap1 and utub_hap2) from PacBio HiFi and chromosome conformation capture (Hi-C) reads into 24 chromosomes; the haplomes are 442 Mbp in size with 35.5 Mbp N50 (for utub_hap1), and 439 Mbp in size with 36.5 Mbp N50 (for utub_hap2). BUSCO results indicate 98.7% and 98% completeness for utub_hap1 and utub_hap2, respectively. We identified Arabidopsis-type telomeric repeats (TTTAGGG) at 40 chromosomal ends out of the 48. Repetitive element annotation reveals that 56.50% and 57.05% of utub_hap1 and utub_hap2 are repetitive, featuring Copia retrotransposons as the most abundant type (12.84% and 12.49%), and also supporting the presence of Helitron transposons (2.78% and 2.97%). Annotation of protein-coding genes based on protein similarity and RNA evidence predicts 28,913 genes and 30,584 transcripts in utub_hap1, and 28,852 genes and 30,696 transcripts in utub_hap2, a difference of only 61 genes between the haplomes. The assemblies will be used to facilitate ongoing research on mutational load, and to study the comparative and evolutionary trajectory of the species and a crop wild relative.