Herbal plants are very important in traditional community use and enrich our plant biodiversity and conservation. Natural products are vital substances of traditional knowledge systems in complementary and alternative medicine, nutraceutical, food supplements, and pharmaceutical bioactive metabolites of new chemical entities. Bioactive secondary metabolites from herbal plants of different forms are main sources and provide major opportunities for drug active pharmaceuticals due to the diverse flora and fauna biodiversity that produces the necessary available chemical diversity. There has been an increasing popularity in phytochemical research within the high through put (HTS) screening programs in search of lead. Phytochemicals of herbal extracts for traditional uses contain various types of bioactive metabolites of pharmaceutical and pharmacotherapeutic nature, and many phytomedicines for different therapeutic areas have been derived from herbal products. This paper is aimed at giving an insight into the extraction, isolation, and characterization of the rich medicinal plant biodiversity of potential pharmaceutical importance and the major drawbacks and challenges in the extraction, isolation, and characterization of phytochemicals in plant extracts. Phytochemicals in medicinal plants have been studied with more emphasis on the extraction process which is a vital stage in the analysis of bioactive compounds in medicinal plant research. The advantages and disadvantages of the different extraction methods is important to discuss following the regulatory guidelines and different pharmacopoeia. The analysis of bioactive molecules in herbal products involves the applications of various phytochemical screening methods, and the use of chromatographic techniques such as TLC and HPLC, including in some cases the non-chromatographic methods like Fourier Transform Infra-Red (FTIR), immunoassay. This paper has been motivated by the challenges faced by most pharmacy students in data mining of information on phytochemical screening and testing of biological activities in projects related to herbal plants research. This write up is also geared towards providing students with information on the preclinical drug discovery process towards the formulation of an improved traditional medicine/ phytomedicine.