High-throughput plant phenotyping, the quantitative measurement of observable plant traits, is critical for modern breeding but remains constrained by a "phenotyping bottleneck," where manual data collection is labor-intensive and prone to observer bias. Conventional closed-set computer vision systems fail to address this challenge, as they require extensive species-specific annotation and lack the flexibility to handle diverse breeding populations. To bridge this gap, we present CropVLM, a Vision-Language Model (VLM) adapted for the agricultural domain via Domain-Specific Semantic Alignment (DSSA). Trained on 52,987 manually selected image-caption pairs covering 37 species in natural field conditions, CropVLM effectively maps agronomic terminology to fine-grained visual features. We further introduce the Hybrid Open-Set Localization Network (HOS-Net), an architecture that integrates CropVLM to enable the detection of novel crops solely from natural language descriptions without retraining. By eliminating the reliance on species-specific training data, CropVLM provides a scalable solution for high-throughput phenotyping, accelerating genetic gain and facilitating large-scale biodiversity research essential for sustainable agriculture. The trained model weights and complete pipeline implementation are publicly available at: [https://github.com/boudiafA/CropVLM](https://github.com/boudiafA/CropVLM). In comprehensive evaluations, CropVLM achieves 72.51% zero-shot classification accuracy, outperforming seven CLIP-style baselines. Our detection pipeline demonstrates superior zero-shot generalization to novel species, achieving 49.17 AP50 on our CVTCropDet benchmark and 50.73 AP50 on tropical fruit species, compared to 34.89 and 48.58 for the next-best method, respectively.