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Lipoxygenases (LOXs) are non-haem iron-containing dioxygenases and play vital roles in a variety of plant biological processes. Here, we first carried out the genome-wide identification of <i>LOX</i> genes in watermelon. A total of 16 <i>LOX</i> genes were identified, which could be classified into two categories according to phylogenetic analysis: the 9-LOXs (ClLOX1–4, 12, and 15) and 13-LOXs (ClLOX5–11, 13, 14, and 16). Furthermore, the protein structures, intrachromosomal distributions, and gene structures were thoroughly analyzed. <i>Cis</i>-element analysis of the promoter regions indicated that the expression of <i>ClLOX</i> genes may be influenced by stress and plant hormones. Bioinformatic and expression analyses revealed that the expression of <i>ClLOX</i> genes is tissue-specific and hormone-responsive. The detected <i>LOX</i> genes exhibited distinctive expression patterns in various tissues. Different <i>ClLOX</i> genes showed different responses to methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ET) treatments, particularly <i>ClLOX7</i>, which exhibited the most active response to the above treatments. This study provides valuable information for a better understanding of the functions of <i>LOX</i> genes and further exploration of the <i>LOX</i> gene family in watermelon.