As the cost of training large language models (LLMs) rises, protecting their intellectual property has become increasingly critical. Model merging, which integrates multiple expert models into a single model capable of performing multiple tasks, presents a growing risk of unauthorized and malicious usage. While fingerprinting techniques have been studied for asserting model ownership, existing methods have primarily focused on fine-tuning, leaving model merging underexplored. To address this gap, we propose a novel fingerprinting method MergePrint that embeds robust fingerprints designed to preserve ownership claims even after model merging. By optimizing against a pseudo-merged model, which simulates post-merged model weights, MergePrint generates fingerprints that remain detectable after merging. Additionally, we optimize the fingerprint inputs to minimize performance degradation, enabling verification through specific outputs from targeted inputs. This approach provides a practical fingerprinting strategy for asserting ownership in cases of misappropriation through model merging.