To address the paucity of available molecularly targeted photoacoustic imaging probes (PIPs) and to generate meaningful data to support the ongoing effort to refine diagnostic photoacoustic imaging (PAI) applications, the work presented here focuses on the design, synthesis, and evaluation of novel PIPs. To this end, various light-absorbing small molecule dyes, targeting strategies, and disease-targeting molecules were evaluated. First, a near-infrared photoacoustic probe was used to image bone in vivo through active and bioorthogonal pre-targeting strategies by utilizing a coupling between a tetrazine-derived cyanine dye and a trans-cyclooctene-modified bisphosphonate. In vitro hydroxyapatite binding and in vivo bone imaging studies showed significant localization of the agent to the target using both active and pre-targeting strategies. The tetrazine-dye building block was then used to create a first-generation bacteria-targeting PIP, using a trans-cyclooctene-modified Zinc (II)-dipicolylamine (ZnDPA). The PIP demonstrated poor aqueous solubility and overlapping photoacoustic (PA) signal with deoxyhemoglobin. Therefore, a commercially available ZnDPA-derived fluorophore, PSVue794, was then repurposed for use as a PIP. PSVue794 demonstrated the ability to differentiate between bacterial infection, sterile inflammation, and healthy tissue in a mouse model, via PA imaging, which prompted its use in a series of proof-of-concept studies towards the generation of a model of implant infection. The feasibility of detecting the PIP in the presence of a PA signal-emitting metallic implant, which was deemed a significant hurdle due to the intensity of the PA signal of the metal, was verified. Although the work requires some follow-up evaluations to demonstrate the practical use of the model, ZnDPA-based PIPs have remained promising candidates for PAI of bacterial infection. Finally, a novel general-purpose dye was designed to possess properties ideal for in vivo PAI. To evaluate the modifications made, the general-purpose dye was conjugated with ZnDPA, and was tested alongside the non-targeted counterpart and PSVue794. Through the studies conducted, it was evident that the rationale that contributed to the design of the general-purpose dye did lead to highly soluble PIP with promising PA properties, however, the PIP did not demonstrate target-specificity, in vivo. Therefore, investigations using the non-targeted PIP with higher affinity targeting vectors for PA-compatible diseases, such as surgical-site/implant infections and prostate cancer, is warranted. / Thesis / Doctor of Philosophy (PhD) / The work conducted within this thesis aims to outline the process of developing photoacoustic diagnostic agents for the detection of various diseases, including bone disease and bacterial infection. To this end, various small molecule, near-infrared absorbing dyes, disease-targeting molecules, and assembly methods were selected to generate several diagnostic agents. To demonstrate their utility, the diagnostic agents were each evaluated in a series of studies designed to assess their ability to generate detectable photoacoustic signal, interact specifically with disease-markers, and localize the sites of disease in living systems. Significant attention was placed on comprehensively evaluating the diagnostic agents through the development of methodology and generating a standard procedure for photoacoustic data production and reporting, which was practiced throughout the work.