Biological multimodal large language models (MLLMs) have emerged as powerful foundation models for scientific discovery. However, existing models are specialized to a single modality, limiting their ability to solve inherently cross-modal scientific problems. While model merging is an efficient method to combine the different modalities into a unified MLLM, existing methods rely on input-agnostic parameter space heuristics that fail to faithfully capture modality specialization. To overcome this limitation, we propose the Embedding-Signal-based MLLM Merging (ES-Merging), a framework that estimates merging coefficients from embedding space signals, moving the merging paradigm from the parameter signals to the embedding signals. ES-Merging exploits coarse-grained and fine-grained signals from embedding space to estimate the layer-wise and element-wise merging coefficients, respectively, which are jointly combined for complementary coefficient estimation. Through extensive experiments, we demonstrate that ES-Merging outperforms existing merging methods not only on the cross-modal reasoning but also on the single-modal knowledge preservation, establishing that embedding space signals provide a principled and effective foundation for MLLM merging.