Carotenoids, polyphenols, and ascorbic acid are valuable and important biologically active compounds that contribute to the health benefits of different foods, and rosehips are known for their high biologically active substance contents. The aim of this research is to identify and compare the contents of carotenoids, polyphenols, and ascorbic acid in the flesh and seeds of different rosehip species grown organically. A field experiment was conducted during the period 2017–2018 on an organic farm in Lithuania. Rose fruits were collected at full ripening in September. The quantitative and qualitative determinations of polyphenols and carotenoids in rosehips flesh and seeds were conducted by HPLC methods. The following polyphenolic compounds were identified: five different flavonoids (rutin, kaempferol-3-O-glucoside, luteolin, quercetin, and quercetin-3-O-glucoside) and five phenolic acids (gallic, chlorogenic, caffeic, p-coumaric, and ferulic) from different rose fruit fleshes and seeds species. In addition, six carotenoids (β-carotene, α-carotene, lutein, zeaxanthin, cis-lycopene, and trans-lycopene) in rosehip flesh and five different carotenoids in rosehip seeds (α-carotene, lutein, zeaxanthin, cis-lycopene, and trans-lycopene) were identified. Overall, the results of this study demonstrate that the highest content of total phenolic acid is in rosehip seeds, while higher concentrations of carotenoids, flavonoids, and ascorbic acid are present in rosehip flesh.