Ultrasound imaging is a relatively low cost, portable and non-invasive medical imaging modality for the diagnosis of a wide spectrum of diseases. Molecular imaging of diseases provide valuable information for improved disease diagnosis and management and has been developed to integrate into various medical imaging platform. However, no molecular probes has been developed for ultrasound imaging to date. In this study, we synthesized gold nano rod (AuNRs) with controllable aspect ratio as the core of molecular probe. The AuNR was modified with poly-ethylene glycol (PEG) and monocolonal antibody specific for the target biomolecules such as Her-2, CXCR4, EGFR in this research. The molecular photoacoustic ultrasonography. The AuNR probe exhibit surface plasmonic resonance frequency (SPR) proportional to their aspect ratio. Two type of AuNR with SPR at 785nm and 1000nm, respectively, were synthesized. The SPR spectra fall into NIR range of biological optical window and thus enabled better tissue penetration of the laser light. Interaction of AuNRs with laser irradiation was able to generate acoustic wave for image reconstruction and precision dynamic measurement of local fluid flow. In vitro study demonstrated a significant photoacoustic molecular imaging of Her-2 in the wild type cancer cells compared to the gene knock down cells mediated by stable transfection of RNAi. The use of molecular probes with different peak SPR frequencies enabled a differential molecular diagnosis of expression level of EGFR or Her2 oncogenes in two cell line models by modulation of laser wavelength. Molecular imaging of cancer bearing animals also obtained primary success with an augmentation in signal intensity from 3db to 5db by using multiple cocktail molecular probes. In addition, AuNR was found to absorb laser light with corresponding SPR frequency to generate local heat at nanometer scale range, which could be applied for precision hyperthermia therapy. AuNRs conjugated HER-2 antibodies successfully target tumor cells of high expression level and induced cancer cell death upon laser irradiation while spare the control cell line of low expression level. A laser wave length guided selective targeting cancer cell therapy was demonstrated using two types of molecular probes (anti-EGFR and anti-Her2) with different peak SPR and four different cancer cell lines. Combined cocktail probes targeting to the same cancer cell significantly improve therapeutic efficacy. In conclusion, a novel AuNR-molecular probe system that combined the power of photoacoustic molecular imaging and targeting therapy in one was developed and demonstrated to be effective. Future preclinical and clinical evaluation is warranted.